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Overview MIPE file
Overview of MIPE file: ../reseqSNPs.mipe
Page created by mipe2html.pl (see http://mipe.sourceforge.net)
Requested PCR products: all
PCR ID: Gene1_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
CAGCTTGTTGTGAGCCAGGGCCAGGCGGGTGAGCGCGGGCAGGCCCTGCAGGGCGGGCAG
AGCCTCCAGCGCGTTGTGGGACAGCAGCAGCTCCTTCAGGCTGGGCAGCgGGGCCTCAGT
GAGCACAGCCTGCAGGCCGTTGTCAGACAGGTCGAGGACCTGCAGGGCGGGCAGCGTCTG
GAAGGTGGCCGTGGAGACGAACAGCAGGCGGTTGGCGTTGAGCAGCAGGATGCCCGTGTC
CTCGGGCAGTGTCTGGAAGGCGGCCGTGGAGAtGGACAGCAGGCGGTTGGCGTTGAGCAG
CAGGATGCCCGTGTtCTCgGGCAGGCTGgCGGGCACCGCaCCGAGATCCcGCCCGGTGCA
GTTCACCTCCACGATGTCCTTCACCTTGTTCATCTCCCAcGGGCAGGGCGGCGGCGGCTC
TGTGGGGACGGCTGCGGGCTGCAGGGCTGtGAGGATCAGCGGGAGCAGAGCGGGAAACCG
CACGGCCTGCGGGGAGAGCCCAGCTGTGTGTGGCTGTGGGTGCAGCCCCGGCCTTGTGGG
CGTCCCAAGCACCCgGACtCAGCACCCAGACCCCAAGCACTCTGAC
pos on source: 392-977
Source
File: sources/Gene1.fas
name: Gene1
species: chicken
Primer1
oligo: OL04-675
seq: CAGCTTGTTGTGAGCCAGG
Tm: 60.60
Primer2
oligo: OL04-676
seq: GTCAGAGTGCTTGGGGTCTG
Tm: 60.86
Use
seq: unknown
revcomp: 0
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| Gene1_1_110 | 110 | | | R | | 1 |
| Gene1_1_273 | 273 | | | | | 1 |
| Gene1_1_315 | 315 | | | | | 1 |
| Gene1_1_319 | 319 | | | | | 1 |
| Gene1_1_329 | 329 | | | | | 1 |
| Gene1_1_340 | 340 | | | | | 1 |
| Gene1_1_350 | 350 | | | | | 1 |
| Gene1_1_400 | 400 | | | | | 1 |
| Gene1_1_450 | 450 | | | | | 1 |
| Gene1_1_555 | 555 | | | | | 1 |
| Gene1_1_559 | 559 | | | | | 1 |
SNP remarks
| remark |
| Gene1_1_110 | exon; non-synonymous |
| Gene1_1_273 | intron |
| Gene1_1_315 | intron |
| Gene1_1_319 | intron |
| Gene1_1_329 | intron |
| Gene1_1_340 | intron |
| Gene1_1_350 | intron |
| Gene1_1_400 | intron |
| Gene1_1_450 | intron |
| Gene1_1_555 | intron |
| Gene1_1_559 | intron |
Samples
No samples
PCR ID: Gene2_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
TCATTTCATGGTGTGTGGCTTCCAACCTTCGGTGTCAGGCTATGAGAAGTGCCCCATCCA
CTTCTGATAAATGCAGTCCCGTTGCCaGGCCTGACTAACATGTATACTTACTGTCTGCAT
ATGCCTTCTTTGCAAACAGAAAGCATTTTTTTTTCCTAGTATAGAAGAAGTACAGGGAGT
AACTTAAAAACATAAAGGATGGCAATGCTTCTGAAGTGAGTTCAGCATCTGTCACCTCTT
GGTTTCCCAGCAGCATACCCaAACCgGGGTGTAAATGCAATATTCaGAGGGGAAAACAGC
CCAGCCGAAATGTCTCCCACATAGGAAGAACAGTACTCACCAAGTTCCTCAGCTTGTTTC
TCTGCAAAACAATGAACAAGCACATATGGGTGTGGGACACCAGCTGGGACATCACCTCTC
CCACAGTCACCTGCAGAGAA
pos on source: 1341-1780
Source
File: sources/Gene2.fas
name: Gene2
species: chicken
Primer1
oligo: OL04-677
seq: TCATTTCATGGTGTGTGGCT
Tm: 59.97
Primer2
oligo: OL04-678
seq: TTCTCTGCAGGTGACTGTGG
Tm: 60.02
Use
seq:
AAGAACAGTACTCACCAAGTTCCTCAGCTTGtttttttctctGCAGGTGACTGTGGGAGA
GGTGATGTCCCAGCTGGTGTCCCACACCCATATGT*GCTTGTTCATTGTTTTGCAGA*GA
AACAAGCTGAGGAACTTGGTGAGTACTGT*TCTTCCTATGTGGGAGACATTTCGGCTGGG
CTGTTTTCCCCTCTGAATATTGCATTTACACCCCGGTTTGGGTATGCTGCTGGGAAACCA
AGAGGTGACAGATGCTGAACTCACTTCAGAAGCATTGC*CATCCTTTATGTTTTTAAGTT
ACTCCCTGT*ACTTCTTCTATACTAG*GAAAAAAAAATGCTTTCTGTTTGCAAAGAAGGC
A*TATGCAGACAGTAAGTATACATGTTAGTCAGGCCCGGCAACGGGACTGCATTTATCAG
AA*GTGG*ATGGGGggcTtctcATAACCTGACACcgaAGgTTGGAAGCCACACACCATGA
AAtgaaaaACAAGCTGAGGAACTTGGTGAGTAcT
revcomp: 1
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| snp_Gene2_1_147 | 147 | 332 | 1672 | Y | 1 | 0 |
| snp_Gene2_1_194 | 194 | 286 | 1626 | K | 2 | 1 |
| snp_Gene2_1_204 | 204 | 276 | 1616 | R | 1 | 0 |
| snp_Gene2_1_207 | 207 | 273 | 1613 | Y | 5 | 0 |
| snp_Gene2_1_214 | 214 | 266 | 1606 | Y | 2 | 1 |
| snp_Gene2_1_215 | 215 | 265 | 1605 | S | 3 | 0 |
| snp_Gene2_1_219 | 219 | 261 | 1601 | Y | 2 | 1 |
| snp_Gene2_1_361 | 361 | 122 | 1462 | R | 1 | 0 |
| snp_Gene2_1_371 | 371 | 113 | 1453 | Y | 1 | 0 |
| snp_Gene2_1_397 | 397 | 87 | 1427 | | | 1 |
SNP remarks
| remark |
| snp_Gene2_1_194 | LLNL_ID=jf1002729; also found by LLNL; Gene2_1_286; amb M; pos 286 on design; exon; non-synonymous |
| snp_Gene2_1_214 | LLNL_ID=jf1002728; also found by LLNL; Gene2_1_266; amb R; pos 266 on design; exon; non-synonymous |
| snp_Gene2_1_219 | LLNL_ID=jf1002727; also found by LLNL; Gene2_1_261; amb R; pos 261 on design; exon; synonymous |
| snp_Gene2_1_397 | only found by LLNL; Gene2_1_87; pos 87 on design; intron |
Samples
Sample meta data
| file |
| sample_1_Gene2-1F_ASP_11F_2718_F02_12.ab1 | 1_Gene2-1F_ASP_11F_2718_F02_12.ab1 |
| sample_1_Gene2-1F_ASP_11M_2734_E02_10.ab1 | 1_Gene2-1F_ASP_11M_2734_E02_10.ab1 |
| sample_1_Gene2-1F_ASP_13F_2774_H02_16.ab1 | 1_Gene2-1F_ASP_13F_2774_H02_16.ab1 |
| sample_1_Gene2-1F_ASP_13M_2757_G02_14.ab1 | 1_Gene2-1F_ASP_13M_2757_G02_14.ab1 |
| sample_1_Gene2-1F_RJF_24_G01_13.ab1 | 1_Gene2-1F_RJF_24_G01_13.ab1 |
| sample_1_Gene2-1F_RJF_29_H01_15.ab1 | 1_Gene2-1F_RJF_29_H01_15.ab1 |
| sample_1_Gene2-1F_S5_O_6030_C01_05.ab1 | 1_Gene2-1F_S5_O_6030_C01_05.ab1 |
| sample_1_Gene2-1F_WL_HF_6144_A02_02.ab1 | 1_Gene2-1F_WL_HF_6144_A02_02.ab1 |
| sample_1_Gene2-1F_WL_LF_7330_D02_08.ab1 | 1_Gene2-1F_WL_LF_7330_D02_08.ab1 |
| sample_1_Gene2-1F_WL_LM_5260_C02_06.ab1 | 1_Gene2-1F_WL_LM_5260_C02_06.ab1 |
| sample_1_Gene2-1R_ASP_11F_2718_F02_12.ab1 | 1_Gene2-1R_ASP_11F_2718_F02_12.ab1 |
| sample_1_Gene2-1R_ASP_11M_2734_E02_10.ab1 | 1_Gene2-1R_ASP_11M_2734_E02_10.ab1 |
| sample_1_Gene2-1R_ASP_13F_2774_H02_16.ab1 | 1_Gene2-1R_ASP_13F_2774_H02_16.ab1 |
| sample_1_Gene2-1R_ASP_13M_2757_G02_14.ab1 | 1_Gene2-1R_ASP_13M_2757_G02_14.ab1 |
| sample_1_Gene2-1R_C44_F_9040_E01_09.ab1 | 1_Gene2-1R_C44_F_9040_E01_09.ab1 |
| sample_1_Gene2-1R_C44_M_2136_D01_07.ab1 | 1_Gene2-1R_C44_M_2136_D01_07.ab1 |
| sample_1_Gene2-1R_C44_O_2136_F01_11.ab1 | 1_Gene2-1R_C44_O_2136_F01_11.ab1 |
| sample_1_Gene2-1R_RJF_24_G01_13.ab1 | 1_Gene2-1R_RJF_24_G01_13.ab1 |
| sample_1_Gene2-1R_S5_F_6030_B01_03.ab1 | 1_Gene2-1R_S5_F_6030_B01_03.ab1 |
| sample_1_Gene2-1R_S5_M_8721_A01_01.ab1 | 1_Gene2-1R_S5_M_8721_A01_01.ab1 |
| sample_1_Gene2-1R_S5_O_6030_C01_05.ab1 | 1_Gene2-1R_S5_O_6030_C01_05.ab1 |
| sample_1_Gene2-1R_WL_HF_6144_A02_02.ab1 | 1_Gene2-1R_WL_HF_6144_A02_02.ab1 |
| sample_1_Gene2-1R_WL_HF_6320_B02_04.ab1 | 1_Gene2-1R_WL_HF_6320_B02_04.ab1 |
| sample_1_Gene2-1R_WL_LF_7330_D02_08.ab1 | 1_Gene2-1R_WL_LF_7330_D02_08.ab1 |
| sample_1_Gene2-1R_WL_LM_5260_C02_06.ab1 | 1_Gene2-1R_WL_LM_5260_C02_06.ab1 |
Sample genotyping data
| 147 | 194 | 204 | 207 | 214 | 215 | 219 | 361 | 371 | 397 |
| sample_1_Gene2-1F_ASP_11F_2718_F02_12.ab1 | T | T | R | T | C | G | T | | | |
| sample_1_Gene2-1F_ASP_11M_2734_E02_10.ab1 | | T | A | T | C | G | T | | | |
| sample_1_Gene2-1F_ASP_13F_2774_H02_16.ab1 | T | T | A | T | C | G | T | A | C | |
| sample_1_Gene2-1F_ASP_13M_2757_G02_14.ab1 | T | T | R | T | C | S | T | | | |
| sample_1_Gene2-1F_RJF_24_G01_13.ab1 | T | T | R | T | C | G | T | G | | |
| sample_1_Gene2-1F_RJF_29_H01_15.ab1 | | T | R | T | C | S | T | | | |
| sample_1_Gene2-1F_S5_O_6030_C01_05.ab1 | Y | T | R | T | C | S | T | A | C | |
| sample_1_Gene2-1F_WL_HF_6144_A02_02.ab1 | Y | T | A | T | C | G | T | G | | |
| sample_1_Gene2-1F_WL_LF_7330_D02_08.ab1 | | T | R | T | C | S | T | | | |
| sample_1_Gene2-1F_WL_LM_5260_C02_06.ab1 | | | R | T | C | S | T | | | |
| sample_1_Gene2-1R_ASP_11F_2718_F02_12.ab1 | T | T | A | T | C | G | T | A | C | |
| sample_1_Gene2-1R_ASP_11M_2734_E02_10.ab1 | T | T | A | T | C | G | T | R | Y | |
| sample_1_Gene2-1R_ASP_13F_2774_H02_16.ab1 | T | T | A | T | C | G | T | A | C | |
| sample_1_Gene2-1R_ASP_13M_2757_G02_14.ab1 | T | T | A | T | C | G | T | R | Y | |
| sample_1_Gene2-1R_C44_F_9040_E01_09.ab1 | T | T | A | T | C | S | T | | | |
| sample_1_Gene2-1R_C44_M_2136_D01_07.ab1 | T | T | A | T | C | G | T | | | |
| sample_1_Gene2-1R_C44_O_2136_F01_11.ab1 | T | T | A | T | C | G | T | | | |
| sample_1_Gene2-1R_RJF_24_G01_13.ab1 | T | T | A | T | C | G | T | R | Y | |
| sample_1_Gene2-1R_S5_F_6030_B01_03.ab1 | Y | T | A | Y | C | G | T | A | C | |
| sample_1_Gene2-1R_S5_M_8721_A01_01.ab1 | Y | K | A | T | Y | G | Y | A | C | |
| sample_1_Gene2-1R_S5_O_6030_C01_05.ab1 | C | T | A | T | C | G | T | A | C | |
| sample_1_Gene2-1R_WL_HF_6144_A02_02.ab1 | Y | T | A | T | C | G | T | R | Y | |
| sample_1_Gene2-1R_WL_HF_6320_B02_04.ab1 | T | T | A | T | T | G | Y | G | Y | |
| sample_1_Gene2-1R_WL_LF_7330_D02_08.ab1 | T | T | A | T | C | G | T | R | Y | |
| sample_1_Gene2-1R_WL_LM_5260_C02_06.ab1 | T | T | A | T | C | G | T | | | |
PCR ID: Gene2_2
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
TCTCAGCTCAACACAGCACCCCTAACCCCCTTAAAGGTTGAACGTTCACATCAAGAAAAA
CTATTAGCCTTTATgCAATGACCACCAGAGACCACCACCACATATTAGGATCCACaCTCA
AGAGGGTGGAACAATATGTTAATAATTTCTCAGAATTCCACCCCATTTTCTTGGAACATA
ATGAATATCTACATGTTATGTCTTTGAATATGTAACCATTGCTTTTCTCAGTGTGTGTTA
GGAGGAGATACCCCCTCGTACCCAGCACCATAATAAACACATCCGCTTTATGTGTGTCAT
GGATGTGCTTATTTGGTTTGGCACATCACAGGCTACAGACCTGTCACCTTCAGCTCCACC
ACAGCCTCGTCGTATCCCAAATCACTACGAACAAGGCAGGTATAACGCCCTCTGTCAGAC
AGCTGCACACGGAAAATTCTCAAGCTCACGCTGCCATTGGCGAGGCCGTCCTTCAGCATC
TCCGTGCGCCCcTGGTACCGGAGCTCCTGGTCCCCATAGTGGTCCTGGCCATCCCTGTAG
CGATGCACGAAGGGTGTGAATTGGTCCCGAAACCACATCACCTCCATGTGCTGCACGCTC
TGCTCCGGGGACAGGTGGCAAGGCAGCACCACGTCCTGCCCCACAGCCACGGCCACAGGG
TCAGGGGGGCCCTGCACGCTGAATGGGACTGGGAGGAAAGCAAGAAATCACTGTGAGCTG
GCTGAAAGTCACTGCTGTGCCACCACATGGGCAGAGCAACCACAGCCACGGGGGCCCATA
CCTGACTGCAGCTCATGAATGCGGAAAACGGAACTGTAAATGACAGCAGCCAGCAGAGAG
CAGCGGAGGCAGCAGCCAAAAAACATCGTCTTCATGGAGCCCAcCCTGAGGATGGAGAAG
GGGAAGTGAAGGGAG
pos on source: 3941-4855
Source
File: sources/Gene2.fas
name: Gene2
species: chicken
Primer1
oligo: OL04-679
seq: TCTCAGCTCAACACAGCACC
Tm: 60.19
Primer2
oligo: OL04-680
seq: CTCCCTTCACTTCCCCTTCT
Tm: 59.67
Use
seq:
GGGCTCCATGAAGACGATGTTTTTTGGCTGCTGCCTCCGCTGCTCTCTGCTGGCTGCTGT
CATTTACAGTTCCGTTTTCCGCATTCATGAGCTGCAGTCAGGTATGGGCCCCCGTGGCTG
TGGTTGCTCTGCCCATGTGGTGGCACAGCAGTGACTTTCAGCCAGCTCACAGTGATTTCT
TGCTTTCCTCCCAGTCCCATTCAGCGTGCAGGGCCCCCCTGACCCTGTGGCCGTGGCTGT
GGGGCAGGACGTGGTGCTGCCTTGCCACCTGTCCCCGGAGCAGAGCGTGCAGCACATGGA
GGTGATGTGGTTTCGGGACCAATTCACACCCTTCGTGCATCGCTACAGGGATGGCCAGGA
CCACTATGGGGACCAGGAGCTCCGGTACCAAGGGCGCACGGAGATGCTGAAGGACGGCCT
CGCCAATGGCACCGTGAGCTTGAGAATTTTCCGTGTGCAGCTGTCTGACAGAGGGCGTTA
TACCTGCCTTGTTCGTAGTGATTTGGGATACGACGAGGCTGTGGTGGAGCTGAAGGTGAC
AGGTCTGTAGCCTGTGATGTGCCAAACCAAATAAGCACATCCATGACACACATAAAGTGG
ATGTGTTTATTATGGTGCTGGATATGAGGGGGTATCTCCTCCTA*ACACACACTGAGAAA
A*GCAATGGTTACATATTCAAAGACATA*ACATGTAGATATTCATTATGTT*CCAAGAAA
ATGGGGAGGAATTCTGAGAAATTATTA*ACATATTGTTCCACCCTCTTGAGCGTGGA*Tc
CTAATATGTGGTGGTGGTCTCTGGTGGTCATTGCATAAAGGCTAAatagTTTTTCTTGAt
g
revcomp: 1
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| snp_Gene2_2_-2 | -2 | | 4824 | | | 1 |
| snp_Gene2_2_11 | 11 | 872 | 4812 | W | 3 | 0 |
| snp_Gene2_2_23 | 23 | 860 | 4800 | Y | 2 | 0 |
| snp_Gene2_2_74 | 74 | 809 | 4749 | R | 3 | 0 |
| snp_Gene2_2_76 | 76 | 807 | 4747 | K | 1 | 0 |
| snp_Gene2_2_77 | 77 | 806 | 4746 | K | 3 | 0 |
| snp_Gene2_2_80 | 80 | 803 | 4743 | Y | 2 | 0 |
| snp_Gene2_2_191 | 191 | 692 | 4632 | Y | 1 | 0 |
| snp_Gene2_2_376 | 376 | 507 | 4447 | S | 3 | 0 |
| snp_Gene2_2_391 | 391 | 492 | 4432 | D | 4 | 1 |
| snp_Gene2_2_395 | 395 | | | Y | 1 | 0 |
| snp_Gene2_2_416 | 416 | 467 | 4407 | R | 1 | 0 |
| snp_Gene2_2_421 | 421 | 462 | 4402 | Y | 2 | 0 |
| snp_Gene2_2_429 | 429 | | | S | 3 | 0 |
| snp_Gene2_2_432 | 432 | 451 | 4391 | S | 1 | 0 |
| snp_Gene2_2_438 | 438 | | | R | 1 | 0 |
| snp_Gene2_2_550 | 550 | 333 | 4273 | S | 3 | 0 |
| snp_Gene2_2_583 | 583 | 300 | 4240 | M | 1 | 0 |
| snp_Gene2_2_584 | 584 | 299 | 4239 | Y | 3 | 0 |
| snp_Gene2_2_598 | 598 | 285 | 4225 | Y | 1 | 0 |
| snp_Gene2_2_599 | 599 | | | R | 1 | 0 |
| snp_Gene2_2_621 | 621 | | | S | 3 | 0 |
| snp_Gene2_2_622 | 622 | | | R | 2 | 0 |
| snp_Gene2_2_624 | 624 | | | M | 1 | 0 |
| snp_Gene2_2_625 | 625 | | | Y | 1 | 0 |
| snp_Gene2_2_647 | 647 | 237 | 4177 | M | 3 | 0 |
| snp_Gene2_2_727 | 727 | 160 | 4100 | H | 1 | 0 |
| snp_Gene2_2_761 | 761 | 127 | 4067 | M | 1 | 0 |
| snp_Gene2_2_772 | 772 | 116 | 4056 | Y | 3 | 1 |
| snp_Gene2_2_814 | 814 | 75 | 4015 | S | 2 | 1 |
SNP remarks
| remark |
| snp_Gene2_2_-2 | only found by LLNL; Gene2_2_884; intron |
| snp_Gene2_2_391 | LLNL_ID=jf1002734; Gene2_2_492; also found by LLNL; exon; synonymous; amb Y |
| snp_Gene2_2_772 | also found by LLNL; Gene2_2_116; intron |
| snp_Gene2_2_814 | also found by LLNL; Gene2_2_75; intron |
Samples
Sample meta data
| file |
| sample_1_Gene2-2F_ASP_11F_2718_F04_12.ab1 | 1_Gene2-2F_ASP_11F_2718_F04_12.ab1 |
| sample_1_Gene2-2F_ASP_11M_2734_E04_10.ab1 | 1_Gene2-2F_ASP_11M_2734_E04_10.ab1 |
| sample_1_Gene2-2F_ASP_13F_2774_H04_16.ab1 | 1_Gene2-2F_ASP_13F_2774_H04_16.ab1 |
| sample_1_Gene2-2F_C44_F_9040_E03_09.ab1 | 1_Gene2-2F_C44_F_9040_E03_09.ab1 |
| sample_1_Gene2-2F_C44_M_2136_D03_07.ab1 | 1_Gene2-2F_C44_M_2136_D03_07.ab1 |
| sample_1_Gene2-2F_C44_O_2136_F03_11.ab1 | 1_Gene2-2F_C44_O_2136_F03_11.ab1 |
| sample_1_Gene2-2F_RJF_24_G03_13.ab1 | 1_Gene2-2F_RJF_24_G03_13.ab1 |
| sample_1_Gene2-2F_RJF_29_H03_15.ab1 | 1_Gene2-2F_RJF_29_H03_15.ab1 |
| sample_1_Gene2-2F_S5_F_6030_B03_03.ab1 | 1_Gene2-2F_S5_F_6030_B03_03.ab1 |
| sample_1_Gene2-2F_S5_M_8721_A03_01.ab1 | 1_Gene2-2F_S5_M_8721_A03_01.ab1 |
| sample_1_Gene2-2F_S5_O_6030_C03_05.ab1 | 1_Gene2-2F_S5_O_6030_C03_05.ab1 |
| sample_1_Gene2-2F_WL_HF_6144_A04_02.ab1 | 1_Gene2-2F_WL_HF_6144_A04_02.ab1 |
| sample_1_Gene2-2F_WL_HF_6320_B04_04.ab1 | 1_Gene2-2F_WL_HF_6320_B04_04.ab1 |
| sample_1_Gene2-2F_WL_LF_7330_D04_08.ab1 | 1_Gene2-2F_WL_LF_7330_D04_08.ab1 |
| sample_1_Gene2-2F_WL_LM_5260_C04_06.ab1 | 1_Gene2-2F_WL_LM_5260_C04_06.ab1 |
| sample_1_Gene2-2R_ASP_11F_2718_F02_12.ab1 | 1_Gene2-2R_ASP_11F_2718_F02_12.ab1 |
| sample_1_Gene2-2R_ASP_11M_2734_E02_10.ab1 | 1_Gene2-2R_ASP_11M_2734_E02_10.ab1 |
| sample_1_Gene2-2R_ASP_13F_2774_H02_16.ab1 | 1_Gene2-2R_ASP_13F_2774_H02_16.ab1 |
| sample_1_Gene2-2R_ASP_13M_2757_G02_14.ab1 | 1_Gene2-2R_ASP_13M_2757_G02_14.ab1 |
| sample_1_Gene2-2R_C44_F_9040_E01_09.ab1 | 1_Gene2-2R_C44_F_9040_E01_09.ab1 |
| sample_1_Gene2-2R_C44_M_2136_D01_07.ab1 | 1_Gene2-2R_C44_M_2136_D01_07.ab1 |
| sample_1_Gene2-2R_C44_O_2136_F01_11.ab1 | 1_Gene2-2R_C44_O_2136_F01_11.ab1 |
| sample_1_Gene2-2R_RJF_24_G01_13.ab1 | 1_Gene2-2R_RJF_24_G01_13.ab1 |
| sample_1_Gene2-2R_RJF_29_H01_15.ab1 | 1_Gene2-2R_RJF_29_H01_15.ab1 |
| sample_1_Gene2-2R_S5_F_6030_B01_03.ab1 | 1_Gene2-2R_S5_F_6030_B01_03.ab1 |
| sample_1_Gene2-2R_S5_M_8721_A01_01.ab1 | 1_Gene2-2R_S5_M_8721_A01_01.ab1 |
| sample_1_Gene2-2R_S5_O_6030_C01_05.ab1 | 1_Gene2-2R_S5_O_6030_C01_05.ab1 |
| sample_1_Gene2-2R_WL_HF_6144_A02_02.ab1 | 1_Gene2-2R_WL_HF_6144_A02_02.ab1 |
| sample_1_Gene2-2R_WL_HF_6320_B02_04.ab1 | 1_Gene2-2R_WL_HF_6320_B02_04.ab1 |
| sample_1_Gene2-2R_WL_LF_7330_D02_08.ab1 | 1_Gene2-2R_WL_LF_7330_D02_08.ab1 |
| sample_1_Gene2-2R_WL_LM_5260_C02_06.ab1 | 1_Gene2-2R_WL_LM_5260_C02_06.ab1 |
Sample genotyping data
| -2 | 11 | 23 | 74 | 76 | 77 | 80 | 191 | 376 | 391 | 395 | 416 | 421 | 429 | 432 | 438 | 550 | 583 | 584 | 598 | 599 | 621 | 622 | 624 | 625 | 647 | 727 | 761 | 772 | 814 |
| sample_1_Gene2-2F_ASP_11F_2718_F04_12.ab1 | | | | | | | | | G | G | C | G | C | S | G | G | G | A | T | T | G | G | G | M | C | C | T | A | C | G |
| sample_1_Gene2-2F_ASP_11M_2734_E04_10.ab1 | | | | | | | | | | | | | | | | | | | | | | | | | | | W | | | |
| sample_1_Gene2-2F_ASP_13F_2774_H04_16.ab1 | | | | | | | | | G | A | Y | R | C | G | S | R | G | M | C | C | G | G | A | A | T | M | T | A | C | C |
| sample_1_Gene2-2F_C44_F_9040_E03_09.ab1 | | | | | | | | | G | A | C | G | C | G | C | G | G | A | T | C | A | G | G | M | C | C | A | M | | |
| sample_1_Gene2-2F_C44_M_2136_D03_07.ab1 | | | | | | | | | | | | | | | | | G | M | Y | C | R | G | R | A | Y | M | W | M | | |
| sample_1_Gene2-2F_C44_O_2136_F03_11.ab1 | | | | | | | | | | | | | | | | G | G | A | Y | C | R | G | A | A | Y | M | W | M | | |
| sample_1_Gene2-2F_RJF_24_G03_13.ab1 | | | | | | | | | | | | | | | | | S | A | Y | C | R | G | G | M | C | C | A | M | | |
| sample_1_Gene2-2F_RJF_29_H03_15.ab1 | | | | | | | | | | | | | | S | S | G | G | A | Y | C | G | G | G | M | C | C | W | M | | |
| sample_1_Gene2-2F_S5_F_6030_B03_03.ab1 | | | | | | | | | G | A | Y | R | Y | G | S | R | G | M | C | C | G | S | A | A | T | C | T | A | C | |
| sample_1_Gene2-2F_S5_M_8721_A03_01.ab1 | | | | | | | | | G | A | C | R | C | S | S | R | G | A | Y | C | G | G | R | A | Y | C | T | A | | |
| sample_1_Gene2-2F_S5_O_6030_C03_05.ab1 | | | | | | | | | G | A | C | R | Y | S | G | R | S | M | C | C | G | S | A | A | T | C | T | M | | |
| sample_1_Gene2-2F_WL_HF_6144_A04_02.ab1 | | | | | | | | | G | A | C | G | C | G | S | G | G | A | T | C | R | G | G | A | C | C | W | A | Y | |
| sample_1_Gene2-2F_WL_HF_6320_B04_04.ab1 | | | | | | | | | | | | | | | | | | | | | | | | | | | T | | | |
| sample_1_Gene2-2F_WL_LF_7330_D04_08.ab1 | | | | | | | | | | | | | | | | | | | | | | | | | | | W | | | |
| sample_1_Gene2-2F_WL_LM_5260_C04_06.ab1 | | | | | | | | | | | | | | | | | | | | | | | | | | | Y | | | |
| sample_1_Gene2-2R_ASP_11F_2718_F02_12.ab1 | | A | T | R | T | T | Y | C | | | | | | | | | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_ASP_11M_2734_E02_10.ab1 | | A | T | R | K | T | Y | C | S | R | C | | | | | | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_ASP_13F_2774_H02_16.ab1 | | A | T | G | K | T | C | C | G | A | Y | R | C | G | S | R | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_ASP_13M_2757_G02_14.ab1 | | W | T | G | K | T | C | C | S | A | Y | | | | | | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_C44_F_9040_E01_09.ab1 | | | T | G | K | T | C | C | G | A | C | G | C | G | C | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_C44_M_2136_D01_07.ab1 | | | T | G | K | K | C | C | S | | | | | | | | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_C44_O_2136_F01_11.ab1 | | A | T | G | K | T | C | C | S | A | C | G | C | G | C | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_RJF_24_G01_13.ab1 | | | | G | K | K | C | C | G | R | C | G | C | G | S | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_RJF_29_H01_15.ab1 | | | | G | K | K | C | C | S | K | C | G | C | G | G | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_S5_F_6030_B01_03.ab1 | | | T | G | K | T | C | C | S | A | Y | R | Y | G | G | R | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_S5_M_8721_A01_01.ab1 | | T | Y | G | K | T | C | Y | G | A | C | R | C | G | G | R | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_S5_O_6030_C01_05.ab1 | | | | G | K | T | C | Y | G | A | C | R | Y | G | G | R | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_WL_HF_6144_A02_02.ab1 | | | T | G | K | K | C | C | G | A | C | G | C | G | S | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_WL_HF_6320_B02_04.ab1 | | | Y | G | K | T | C | C | S | G | C | G | C | G | G | A | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_WL_LF_7330_D02_08.ab1 | | | | G | T | T | C | C | S | A | C | G | C | G | S | G | | | | | | | | | | | | | | |
| sample_1_Gene2-2R_WL_LM_5260_C02_06.ab1 | | A | T | G | K | T | C | C | C | A | | | | | | | | | | | | | | | | | | | | |
PCR ID: Gene3_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
GCCAGCAATCAGACTTGACACTTCTAAGAGCAGTAAAgAATCTGAAGTTAAAACACGTTG
TTTTGATTATTGAAAATAGCTTTCCAAATATAGGAGTTTCTTCATCAAATTCTGTAAAAG
CCTATGGAGTTCTTAACATGTTCACTGTGTATTGAgTACGATACAAACACATTGAAAGAC
TGAGAGAATGGtAAAGAAAAATAAAGAGGCATCCTGTTATTTTTTTTCTCCTCCCTCGAA
GGTGAGAGCTGGCACAATTTTTGACAATTTCTTGATAACGGaTGATGAGGACTATGCAGA
AGACTTTGGAGATGAAACaTGGGGAGAAACAAAGGTAATGTGTGAAATTCTTATCAGTCT
CAGTTCTTTaTTGCCACgTTAAGAGTTGTGTGTAATCTGCGCGATGTTCTATTGGTGCAC
AAAAATGAAATCTTAACTTTAGGATCCTGAAAAGGAAATGAACATAAGGCAGGCTGAAGA
GG
pos on source: 220-701
Source
File: sources/Gene3.fas
name: Gene3
species: chicken
Primer1
oligo: OL04-681
seq: GCCAGCAATCAGACTTGACA
Tm: 59.99
Primer2
oligo: OL04-682
seq: CCTCTTCAGCCTGCCTTATG
Tm: 59.97
Use
seq:
TCagcCTGCCTTATGTTCATTTCCTTTTCAGGATCCTAAAGTTAAGATTTCATTTTTGTG
CACCAATAGAACATCGCGCAGATTACACACAACTCTTAATGTGGCAACAAAGAACTGAGA
CTGATAAGAATTTCACACATTACCTTTGTTTCTCCCCACGTTTCATCTCCAAAGTCTTCT
GCATAGTCCT*CATCATCCGTTATCAAGAAATTGTCAAAAATTGTGCCAGCTCTCACCTT
CGAGGGAGGAGGAAAAAAAAATAACAGGATGCCTC*T**ATTTTTCTTTACCGTTCTCCT
CTCAGTCTTTCAATGTGTTTGTATCGTATTCAATACACAGTGAACATGTTAAGAAC*T*C
CATAGGCTTTTACAGAATTTGATGAAGAAAC*TCCTATATTTGGAAAGC*TATTTTCAAT
A*ATCAAAACAA*CGTGTTTTAACTTCAGATTCTTTACTGCTCTTAGAAGTGTCAAGTCT
GATTGCTGGC
revcomp: 1
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| snp_Gene3_1_100 | 100 | | 597 | Y | 1 | 1 |
| snp_Gene3_1_107 | 107 | | | M | 3 | 0 |
| snp_Gene3_1_108 | 108 | | 589 | Y | 1 | 1 |
| snp_Gene3_1_158 | 158 | | | M | 3 | 0 |
| snp_Gene3_1_159 | 159 | 319 | 538 | Y | 1 | 1 |
| snp_Gene3_1_197 | 197 | 282 | 501 | Y | 4 | 1 |
| snp_Gene3_1_199 | 199 | 280 | 499 | Y | 1 | 0 |
| snp_Gene3_1_241 | 241 | 238 | 457 | Y | 1 | 0 |
| snp_Gene3_1_280 | 280 | | | W | 3 | 0 |
| snp_Gene3_1_290 | 290 | | 411 | | | 1 |
| snp_Gene3_1_292 | 292 | | | Y | 3 | 0 |
| snp_Gene3_1_293 | 293 | | | R | 1 | 0 |
| snp_Gene3_1_294 | 294 | | | B | 3 | 0 |
| snp_Gene3_1_310 | 310 | 175 | 394 | Y | 1 | 0 |
| snp_Gene3_1_329 | 329 | 156 | 375 | Y | 1 | 1 |
| snp_Gene3_1_435 | 435 | 56 | 275 | R | 1 | 0 |
| snp_Gene3_1_453 | 453 | 38 | 257 | M | 2 | 1 |
SNP remarks
| remark |
| snp_Gene3_1_100 | also found by LLNL; Gene3_1_378; pos 378 on design; intron |
| snp_Gene3_1_108 | also found by LLNL; Gene3_1_370; pos 370 on design; intron |
| snp_Gene3_1_159 | LLNL_ID=jf1010739; also found by LLNL; Gene3_1_319; amb R; pos 319 on design; exon; synonymous |
| snp_Gene3_1_197 | LLNL_ID=jf1010738; only found by LLNL; Gene3_1_282; amb R; pos 282 on design; exon; non-synonymous |
| snp_Gene3_1_290 | only found by LLNL; Gene3_1_192; pos 192 on design; intron |
| snp_Gene3_1_329 | also found by LLNL; Gene3_1_156; pos 156 on design; intron |
| snp_Gene3_1_453 | also found by LLNL; Gene3_1_38; pos 38 on design; intron |
Samples
Sample meta data
| file |
| sample_1_Gene3-1F_ASP_11F_2718_F04_12.ab1 | 1_Gene3-1F_ASP_11F_2718_F04_12.ab1 |
| sample_1_Gene3-1F_ASP_11M_2734_E04_10.ab1 | 1_Gene3-1F_ASP_11M_2734_E04_10.ab1 |
| sample_1_Gene3-1F_ASP_13F_2774_H04_16.ab1 | 1_Gene3-1F_ASP_13F_2774_H04_16.ab1 |
| sample_1_Gene3-1F_ASP_13M_2757_G04_14.ab1 | 1_Gene3-1F_ASP_13M_2757_G04_14.ab1 |
| sample_1_Gene3-1F_C44_F_9040_E03_09.ab1 | 1_Gene3-1F_C44_F_9040_E03_09.ab1 |
| sample_1_Gene3-1F_C44_M_2136_D03_07.ab1 | 1_Gene3-1F_C44_M_2136_D03_07.ab1 |
| sample_1_Gene3-1F_C44_O_2136_F03_11.ab1 | 1_Gene3-1F_C44_O_2136_F03_11.ab1 |
| sample_1_Gene3-1F_RJF_24_G03_13.ab1 | 1_Gene3-1F_RJF_24_G03_13.ab1 |
| sample_1_Gene3-1F_RJF_29_H03_15.ab1 | 1_Gene3-1F_RJF_29_H03_15.ab1 |
| sample_1_Gene3-1F_S5_F_6030_B03_03.ab1 | 1_Gene3-1F_S5_F_6030_B03_03.ab1 |
| sample_1_Gene3-1F_S5_M_8721_A03_01.ab1 | 1_Gene3-1F_S5_M_8721_A03_01.ab1 |
| sample_1_Gene3-1F_S5_O_6030_C03_05.ab1 | 1_Gene3-1F_S5_O_6030_C03_05.ab1 |
| sample_1_Gene3-1F_WL_HF_6144_A04_02.ab1 | 1_Gene3-1F_WL_HF_6144_A04_02.ab1 |
| sample_1_Gene3-1F_WL_HF_6320_B04_04.ab1 | 1_Gene3-1F_WL_HF_6320_B04_04.ab1 |
| sample_1_Gene3-1F_WL_LF_7330_D04_08.ab1 | 1_Gene3-1F_WL_LF_7330_D04_08.ab1 |
| sample_1_Gene3-1F_WL_LM_5260_C04_06.ab1 | 1_Gene3-1F_WL_LM_5260_C04_06.ab1 |
| sample_1_Gene3-1R_ASP_11F_2718_F04_12.ab1 | 1_Gene3-1R_ASP_11F_2718_F04_12.ab1 |
| sample_1_Gene3-1R_ASP_11M_2734_E04_10.ab1 | 1_Gene3-1R_ASP_11M_2734_E04_10.ab1 |
| sample_1_Gene3-1R_ASP_13F_2774_H04_16.ab1 | 1_Gene3-1R_ASP_13F_2774_H04_16.ab1 |
| sample_1_Gene3-1R_ASP_13M_2757_G04_14.ab1 | 1_Gene3-1R_ASP_13M_2757_G04_14.ab1 |
| sample_1_Gene3-1R_C44_F_9040_E03_09.ab1 | 1_Gene3-1R_C44_F_9040_E03_09.ab1 |
| sample_1_Gene3-1R_C44_M_2136_D03_07.ab1 | 1_Gene3-1R_C44_M_2136_D03_07.ab1 |
| sample_1_Gene3-1R_C44_O_2136_F03_11.ab1 | 1_Gene3-1R_C44_O_2136_F03_11.ab1 |
| sample_1_Gene3-1R_RJF_24_G03_13.ab1 | 1_Gene3-1R_RJF_24_G03_13.ab1 |
| sample_1_Gene3-1R_RJF_29_H03_15.ab1 | 1_Gene3-1R_RJF_29_H03_15.ab1 |
| sample_1_Gene3-1R_S5_F_6030_B03_03.ab1 | 1_Gene3-1R_S5_F_6030_B03_03.ab1 |
| sample_1_Gene3-1R_S5_M_8721_A03_01.ab1 | 1_Gene3-1R_S5_M_8721_A03_01.ab1 |
| sample_1_Gene3-1R_S5_O_6030_C03_05.ab1 | 1_Gene3-1R_S5_O_6030_C03_05.ab1 |
| sample_1_Gene3-1R_WL_HF_6144_A04_02.ab1 | 1_Gene3-1R_WL_HF_6144_A04_02.ab1 |
| sample_1_Gene3-1R_WL_HF_6320_B04_04.ab1 | 1_Gene3-1R_WL_HF_6320_B04_04.ab1 |
| sample_1_Gene3-1R_WL_LF_7330_D04_08.ab1 | 1_Gene3-1R_WL_LF_7330_D04_08.ab1 |
| sample_1_Gene3-1R_WL_LM_5260_C04_06.ab1 | 1_Gene3-1R_WL_LM_5260_C04_06.ab1 |
Sample genotyping data
| 100 | 107 | 108 | 158 | 159 | 197 | 199 | 241 | 280 | 290 | 292 | 293 | 294 | 310 | 329 | 435 | 453 |
| sample_1_Gene3-1F_ASP_11F_2718_F04_12.ab1 | C | M | C | M | C | Y | C | C | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_ASP_11M_2734_E04_10.ab1 | T | M | C | M | C | T | T | | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_ASP_13F_2774_H04_16.ab1 | T | M | C | M | C | T | T | C | A | | C | G | T | T | T | G | A |
| sample_1_Gene3-1F_ASP_13M_2757_G04_14.ab1 | Y | M | C | M | C | T | Y | C | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_C44_F_9040_E03_09.ab1 | T | M | C | M | C | T | T | C | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_C44_M_2136_D03_07.ab1 | T | M | C | M | C | T | T | C | A | | C | G | T | T | T | G | A |
| sample_1_Gene3-1F_C44_O_2136_F03_11.ab1 | T | M | C | M | C | T | T | Y | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_RJF_24_G03_13.ab1 | | | | | | | | | A | | Y | G | T | T | T | A | C |
| sample_1_Gene3-1F_RJF_29_H03_15.ab1 | | | | | | | | | | | Y | R | Y | T | Y | | |
| sample_1_Gene3-1F_S5_F_6030_B03_03.ab1 | C | M | C | M | C | Y | C | | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_S5_M_8721_A03_01.ab1 | C | M | C | M | C | T | C | C | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_S5_O_6030_C03_05.ab1 | C | M | C | M | C | Y | C | C | A | | C | G | T | T | T | | |
| sample_1_Gene3-1F_WL_HF_6144_A04_02.ab1 | C | A | Y | A | Y | T | C | T | A | | C | R | T | Y | Y | G | C |
| sample_1_Gene3-1F_WL_HF_6320_B04_04.ab1 | C | A | Y | A | Y | Y | C | T | A | | C | R | T | Y | Y | | |
| sample_1_Gene3-1F_WL_LF_7330_D04_08.ab1 | | | | | | | | | | | | | | Y | T | | |
| sample_1_Gene3-1F_WL_LM_5260_C04_06.ab1 | C | M | C | M | C | Y | C | T | A | | C | G | T | T | T | A | C |
| sample_1_Gene3-1R_ASP_11F_2718_F04_12.ab1 | C | A | C | A | C | T | C | C | A | | C | G | T | T | T | G | C |
| sample_1_Gene3-1R_ASP_11M_2734_E04_10.ab1 | T | A | C | A | C | T | T | C | A | | C | G | K | T | T | G | A |
| sample_1_Gene3-1R_ASP_13F_2774_H04_16.ab1 | T | A | C | A | C | T | T | C | A | | C | G | T | T | T | G | A |
| sample_1_Gene3-1R_ASP_13M_2757_G04_14.ab1 | Y | A | C | A | C | T | Y | C | A | | C | G | K | T | T | G | M |
| sample_1_Gene3-1R_C44_F_9040_E03_09.ab1 | T | A | C | A | C | T | T | C | A | | C | G | K | T | T | G | A |
| sample_1_Gene3-1R_C44_M_2136_D03_07.ab1 | T | A | C | A | C | T | T | C | A | | C | G | K | T | T | G | A |
| sample_1_Gene3-1R_C44_O_2136_F03_11.ab1 | T | A | C | A | C | T | T | C | A | | C | G | K | T | T | G | A |
| sample_1_Gene3-1R_RJF_24_G03_13.ab1 | C | A | C | A | C | T | Y | T | | | | | | | | | |
| sample_1_Gene3-1R_RJF_29_H03_15.ab1 | C | A | Y | A | Y | T | C | C | W | | | | | | | | |
| sample_1_Gene3-1R_S5_F_6030_B03_03.ab1 | C | A | C | A | C | T | C | C | A | | C | G | K | T | T | G | C |
| sample_1_Gene3-1R_S5_M_8721_A03_01.ab1 | C | A | C | A | C | T | C | C | A | | C | G | K | T | T | G | C |
| sample_1_Gene3-1R_S5_O_6030_C03_05.ab1 | C | A | C | A | C | T | C | C | A | | C | G | K | T | T | G | C |
| sample_1_Gene3-1R_WL_HF_6144_A04_02.ab1 | C | A | Y | A | Y | T | C | Y | A | | C | R | T | Y | Y | G | C |
| sample_1_Gene3-1R_WL_HF_6320_B04_04.ab1 | C | A | Y | A | T | T | C | Y | A | | C | R | T | Y | Y | G | C |
| sample_1_Gene3-1R_WL_LF_7330_D04_08.ab1 | C | A | C | A | C | T | C | | | | | | | | | | |
| sample_1_Gene3-1R_WL_LM_5260_C04_06.ab1 | C | A | C | A | C | T | C | T | A | | C | G | K | T | T | A | C |
PCR ID: Gene4_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
GAGTGGTTTGGGGCAAAGTAAGGATTCCTCCACAGACACATCGCATGCATCCtCGGACAA
TATGGAGAATGACTGCCAGCTGAATTCAGATGTGAATTTTGTTCCGAAACTTGTTAACGG
AAAGGGTCCGTTAGACCACTTTATACaGAAGAGCACAAAAGATAACACAGATGAAATCAT
CGTCATTATTGACTCGGTAGATGAGTCTAATCAAAGACTCAGTGATGATGTAGACCATGT
TAGTTTTGATTCAAAAGCATCTTCTGCAGCTCTGACTAAtGGTATGCTAGGAAAAGATAC
gAACAAGCTGAGTTGTCTGAATTCCACTCAGAATAGCCAAACTGATGATTCAATGCAGAC
TGATGTGCCGTGTGAAGCTATTGCAAA
pos on source: 449-835
Source
File: sources/Gene4.fas
name: Gene4
species: chicken
Primer1
oligo: OL04-683
seq: GAGTGGTTTGGGGCAAAGTA
Tm: 59.97
Primer2
oligo: OL04-684
seq: TTTGCAATAGCTTCACACGG
Tm: 59.87
Use
seq:
aGTGGTTTGGGGCAAAGTAAGGATTCCTCCACAGACACATCGCATGCATCCACGG*ACAA
TATGGAGAATGACTGCCAGCTGAATTCAGATGTGAATTTTGTTCCGAAACTTGTTAACGG
AAAGGGTCCGTTAGACCACTT*TATACGGAAGAGCACAAAAGATAACACAGATGAAATCA
TTGTCATTATTGACTCGGTAGATGAGTCTAATCAAAGACTCAGTGATGATGTAGAC*CAT
GTTAGTTTTGATTCAAAAGCATCTTCTGCAGCTCTGACTAATGGTATGCTAGGAAAAGAT
ACGAACAAGCTGAGTTGTCTGAATTCCACTCAGAATAGCCAAACTGATGATTCAATGCAG
ACTGATGTGCCGTGTGAAGCTAtTGCAAA
revcomp: 0
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| snp_Gene4_1_52 | 52 | 53 | 501 | W | 4 | 1 |
| snp_Gene4_1_127 | 127 | 127 | 575 | B | 3 | 0 |
| snp_Gene4_1_148 | 148 | 147 | 595 | R | 1 | 1 |
| snp_Gene4_1_175 | 175 | | | R | 1 | 0 |
| snp_Gene4_1_182 | 182 | 181 | 629 | Y | 1 | 0 |
| snp_Gene4_1_282 | 282 | 280 | 728 | Y | 1 | 1 |
| snp_Gene4_1_303 | 303 | 301 | 749 | R | 1 | 1 |
| snp_Gene4_1_318 | 318 | 316 | 764 | K | 3 | 0 |
| snp_Gene4_1_366 | 366 | 364 | 812 | Y | 2 | 0 |
SNP remarks
| remark |
| snp_Gene4_1_52 | LLNL_ID=jf1005911; also found by LLNL; Gene4_1_53; amb W; pos 53 on design; exon; non-synonymous |
| snp_Gene4_1_148 | LLNL_ID=jf1005912; also found by LLNL; Gene4_1_147; amb R; pos 147 on design; exon; non-synonymous |
| snp_Gene4_1_282 | LLNL_ID=jf1005913; also found by LLNL; Gene4_1_280; amb Y; pos 280 on design; exon; synonymous |
| snp_Gene4_1_303 | LLNL_ID=jf1005914; also found by LLNL; Gene4_1_301; amb R; pos 301 on design; exon; synonymous |
Samples
Sample meta data
| file |
| sample_1_Gene4-1F_ASP_11F_2718_F06_12.ab1 | 1_Gene4-1F_ASP_11F_2718_F06_12.ab1 |
| sample_1_Gene4-1F_ASP_11M_2734_E06_10.ab1 | 1_Gene4-1F_ASP_11M_2734_E06_10.ab1 |
| sample_1_Gene4-1F_ASP_13F_2774_H06_16.ab1 | 1_Gene4-1F_ASP_13F_2774_H06_16.ab1 |
| sample_1_Gene4-1F_C44_F_9040_E05_09.ab1 | 1_Gene4-1F_C44_F_9040_E05_09.ab1 |
| sample_1_Gene4-1F_C44_O_2136_F05_11.ab1 | 1_Gene4-1F_C44_O_2136_F05_11.ab1 |
| sample_1_Gene4-1F_RJF_24_G05_13.ab1 | 1_Gene4-1F_RJF_24_G05_13.ab1 |
| sample_1_Gene4-1F_RJF_29_H05_15.ab1 | 1_Gene4-1F_RJF_29_H05_15.ab1 |
| sample_1_Gene4-1F_S5_F_6030_B05_03.ab1 | 1_Gene4-1F_S5_F_6030_B05_03.ab1 |
| sample_1_Gene4-1F_S5_M_8721_A05_01.ab1 | 1_Gene4-1F_S5_M_8721_A05_01.ab1 |
| sample_1_Gene4-1F_S5_O_6030_C05_05.ab1 | 1_Gene4-1F_S5_O_6030_C05_05.ab1 |
| sample_1_Gene4-1F_WL_HF_6144_A06_02.ab1 | 1_Gene4-1F_WL_HF_6144_A06_02.ab1 |
| sample_1_Gene4-1F_WL_HF_6320_B06_04.ab1 | 1_Gene4-1F_WL_HF_6320_B06_04.ab1 |
| sample_1_Gene4-1F_WL_LF_7330_D06_08.ab1 | 1_Gene4-1F_WL_LF_7330_D06_08.ab1 |
| sample_1_Gene4-1F_WL_LM_5260_C06_06.ab1 | 1_Gene4-1F_WL_LM_5260_C06_06.ab1 |
| sample_1_Gene4-1R_ASP_11M_2734_E06_10.ab1 | 1_Gene4-1R_ASP_11M_2734_E06_10.ab1 |
| sample_1_Gene4-1R_ASP_13F_2774_H06_16.ab1 | 1_Gene4-1R_ASP_13F_2774_H06_16.ab1 |
| sample_1_Gene4-1R_ASP_13M_2757_G06_14.ab1 | 1_Gene4-1R_ASP_13M_2757_G06_14.ab1 |
| sample_1_Gene4-1R_C44_F_9040_E05_09.ab1 | 1_Gene4-1R_C44_F_9040_E05_09.ab1 |
| sample_1_Gene4-1R_C44_M_2136_D05_07.ab1 | 1_Gene4-1R_C44_M_2136_D05_07.ab1 |
| sample_1_Gene4-1R_C44_O_2136_F05_11.ab1 | 1_Gene4-1R_C44_O_2136_F05_11.ab1 |
| sample_1_Gene4-1R_RJF_24_G05_13.ab1 | 1_Gene4-1R_RJF_24_G05_13.ab1 |
| sample_1_Gene4-1R_RJF_29_H05_15.ab1 | 1_Gene4-1R_RJF_29_H05_15.ab1 |
| sample_1_Gene4-1R_S5_M_8721_A05_01.ab1 | 1_Gene4-1R_S5_M_8721_A05_01.ab1 |
| sample_1_Gene4-1R_S5_O_6030_C05_05.ab1 | 1_Gene4-1R_S5_O_6030_C05_05.ab1 |
| sample_1_Gene4-1R_WL_HF_6144_A06_02.ab1 | 1_Gene4-1R_WL_HF_6144_A06_02.ab1 |
| sample_1_Gene4-1R_WL_LF_7330_D06_08.ab1 | 1_Gene4-1R_WL_LF_7330_D06_08.ab1 |
| sample_1_Gene4-1R_WL_LM_5260_C06_06.ab1 | 1_Gene4-1R_WL_LM_5260_C06_06.ab1 |
Sample genotyping data
| 52 | 127 | 148 | 175 | 182 | 282 | 303 | 318 | 366 |
| sample_1_Gene4-1F_ASP_11F_2718_F06_12.ab1 | | K | G | A | C | T | G | K | T |
| sample_1_Gene4-1F_ASP_11M_2734_E06_10.ab1 | | K | R | A | C | T | G | K | T |
| sample_1_Gene4-1F_ASP_13F_2774_H06_16.ab1 | A | T | G | A | C | T | G | T | T |
| sample_1_Gene4-1F_C44_F_9040_E05_09.ab1 | | | A | A | C | T | G | K | |
| sample_1_Gene4-1F_C44_O_2136_F05_11.ab1 | | K | R | A | C | T | G | K | T |
| sample_1_Gene4-1F_RJF_24_G05_13.ab1 | A | T | G | A | T | T | G | K | T |
| sample_1_Gene4-1F_RJF_29_H05_15.ab1 | | Y | R | A | Y | T | G | T | T |
| sample_1_Gene4-1F_S5_F_6030_B05_03.ab1 | A | K | G | A | C | Y | R | K | T |
| sample_1_Gene4-1F_S5_M_8721_A05_01.ab1 | A | T | R | R | C | Y | R | T | Y |
| sample_1_Gene4-1F_S5_O_6030_C05_05.ab1 | A | T | R | R | C | T | G | K | Y |
| sample_1_Gene4-1F_WL_HF_6144_A06_02.ab1 | A | T | G | A | C | T | G | T | T |
| sample_1_Gene4-1F_WL_HF_6320_B06_04.ab1 | A | T | G | A | C | T | G | K | T |
| sample_1_Gene4-1F_WL_LF_7330_D06_08.ab1 | | K | G | A | C | T | G | K | |
| sample_1_Gene4-1F_WL_LM_5260_C06_06.ab1 | | K | G | A | C | T | G | | |
| sample_1_Gene4-1R_ASP_11M_2734_E06_10.ab1 | | | R | A | C | T | G | T | |
| sample_1_Gene4-1R_ASP_13F_2774_H06_16.ab1 | A | T | G | A | C | T | G | T | |
| sample_1_Gene4-1R_ASP_13M_2757_G06_14.ab1 | A | T | G | A | C | T | G | T | |
| sample_1_Gene4-1R_C44_F_9040_E05_09.ab1 | A | T | A | A | C | T | G | T | |
| sample_1_Gene4-1R_C44_M_2136_D05_07.ab1 | A | T | A | A | C | T | G | T | |
| sample_1_Gene4-1R_C44_O_2136_F05_11.ab1 | A | T | A | A | C | T | G | T | |
| sample_1_Gene4-1R_RJF_24_G05_13.ab1 | A | T | G | A | T | T | G | T | |
| sample_1_Gene4-1R_RJF_29_H05_15.ab1 | W | T | R | A | Y | T | G | | |
| sample_1_Gene4-1R_S5_M_8721_A05_01.ab1 | A | T | R | R | C | Y | R | T | |
| sample_1_Gene4-1R_S5_O_6030_C05_05.ab1 | A | T | R | R | C | T | G | T | |
| sample_1_Gene4-1R_WL_HF_6144_A06_02.ab1 | A | T | G | A | C | T | G | T | |
| sample_1_Gene4-1R_WL_LF_7330_D06_08.ab1 | A | T | G | A | C | T | G | T | |
| sample_1_Gene4-1R_WL_LM_5260_C06_06.ab1 | A | T | G | A | C | T | G | T | |
PCR ID: Gene5_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
TAAGAGCACTGTGGGGTCCTCTGGGCGGGGTGGCAGAACCCCAATGCCACCCCCTCACCC
CAAGCgTCACTTACTGTGGCCAACCTCCTCCTCCACCTCaTTGGAAAGTGGGTAGGGACC
TCCTCTATGGGGGCTCTCAGCACTGGGACGGGTGATGCTCCACaTCTCCACtGCATTGGC
TGCAGCCCCCTTCACCTCCAGGGCCAGGATGGGGGCCTGGGTGACTGTCCCCACTGGGTC
CTCGGCCACTGTGTGGTCACCGGCCACTGTGGGGTCCTGGACCACCGAGGGGTCCCGGCT
CTGCTGCTGCAGCTGGAAGTAGCGCCCATTCAGCCCAGCGTAGCTGCTCTGTTTTGGGGT
GCCGGGGGTTTCTGCTGCCACAATGGGGACTGTCCCCAAAGCCGGTGCTGCTGGTGGCAA
GCTGGTGACCTCCTGGGCTGGACTTTGGGTCTGTGGATGCAGGGTGAACAGAGGCTCTGT
GGGGTCGGGGAATTCTCGCAGCGCCGGTGCTGGGCTGGTGCCAAACAGCTCCCGTGGGGA
GCCCCGCAGCGCCGGGTCCACCGCATTcAGGGCTTCATCCTCGAGCGGCCGCACCGATGA
GGACGGGGAGGATGCGGAGGCCATGCTGCTGCCCCCGGGGATGTCACCGCGCCACGCTGC
CGTCACACTGCTTGCCcACCGCAACTGCTCGTCCTCGGCACCAcCCGGCCCTGCAGCCCC
CAGCTGCGGCAGGACGCCGGCACGTGGGCTGTCCCCGGAGGTGGCCATGTCCTCATGCTC
CACCAGCACGTTGTCACTGCCCAGCGGCTCCAGTTCCCTCTGCTCTG
pos on source: 2283-3109
Source
File: sources/Gene5.fas
name: Gene5
species: chicken
Primer1
oligo: OL04-685
seq: TAAGAGCACTGTGGGGTCCT
Tm: 59.72
Primer2
oligo: OL04-686
seq: CAGAGCAGAGGGAACTGGAG
Tm: 60.13
Use
seq: unknown
revcomp: 0
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| Gene5_1_66 | 66 | | | | | 1 |
| Gene5_1_100 | 100 | | | R | | 1 |
| Gene5_1_164 | 164 | | | R | | 1 |
| Gene5_1_172 | 172 | | | Y | | 1 |
| Gene5_1_568 | 568 | | | S | | 1 |
| Gene5_1_677 | 677 | | | M | | 1 |
| Gene5_1_704 | 704 | | | Y | | 1 |
SNP remarks
| remark |
| Gene5_1_66 | intron |
| Gene5_1_100 | exon; synonymous |
| Gene5_1_164 | exon; non-synonymous |
| Gene5_1_172 | exon; synonymous |
| Gene5_1_568 | exon; synonymous |
| Gene5_1_677 | exon; non-synonymous |
| Gene5_1_704 | exon; non-synonymous |
Samples
No samples
PCR ID: Gene5_2
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
CTCCAGTTCCCTCTGCTCTGCGGAGGAATCGGGAGCACCCGCCGCGTCCCCTGCAGGGAT
GGGGACTGGGGGTGAGCCGCTGTCTGGCACACAGCAGCGGCCCCGAGGCCaATCCTcGTT
ACCTTTATAGCAGTACGCATCGAACTTGGAGGCAGGCAGAGGGAAGCCGGTGCGGTTGGG
GAAGCGGTAGAGAGTCCGGACGCCCGGCGCCTCCCCGCCACACTTCCTACGTGGAGCCAG
GATGGGGTACCTCACGCTGCCATCCGCCAGCCAGCCCGGGTCACACTGGTCCAGGCCCTC
ACGCCAGGCCAGGTACAGCTGCCCtGTGGTGGCCAACGCAGCCCCACGGCCCCGGCAGTG
CCTCCGCGCCCCCGATAAGGTGAAGCGCCCTGGGGCTGTGGCATAGAACACCTTCCCTGC
AAGAGAGCGCGGCGCATTGGATGGCCGTCCCCATCGCCACGGCGGCACCGAGCGCACCGA
GAGATGTCCCACGCATCCCCCAGTGCTGCTTGCCTTGCAGCTCCCGTGCGTAGCAGTAGA
CATCGTACAGCTCGCCgGGCTCCCTCTGGCCGTAGCTGCGCACCCCgGGGAGGCTGTTGC
GGTCCCCATAGCAGCCGGGTCGGGACAGTGTGATGGGGTACCTGCGGGACAGGCTGGGTG
GGTGCCCGGCTCCGTGCCACCCGCGGTGAGGGGTGCCCGTGCCACGCACTTACCGCACAC
TCTGGTCGGCCAGCCAGCCcGCATCACAGTTGTCATAGCCGTCCTCG
pos on source: 3090-3856
Source
File: sources/Gene5.fas
name: Gene5
species: chicken
Primer1
oligo: OL04-687
seq: CTCCAGTTCCCTCTGCTCTG
Tm: 60.13
Primer2
oligo: OL04-688
seq: CGAGGACGGCTATGACAACT
Tm: 60.28
Use
seq: unknown
revcomp: 0
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| Gene5_2_111 | 111 | | | | | 1 |
| Gene5_2_117 | 117 | | | | | 1 |
| Gene5_2_325 | 325 | | | Y | | 1 |
| Gene5_2_557 | 557 | | | R | | 1 |
| Gene5_2_587 | 587 | | | R | | 1 |
| Gene5_2_740 | 740 | | | Y | | 1 |
SNP remarks
| remark |
| Gene5_2_111 | intron |
| Gene5_2_117 | intron |
| Gene5_2_325 | exon; synonymous |
| Gene5_2_557 | exon; synonymous |
| Gene5_2_587 | exon; synonymous |
| Gene5_2_740 | exon; synonymous |
Samples
No samples
PCR ID: Gene5_3
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
CCACTGAACCGTATCCCTCAGTACAACAGCTAACCATGCACAGCTTGCAGAGGGTGCgCA
ACTCACATACAGTGCACAGCTTGTAGGGTGTGCACGGCTTGCATGGGTGCACAGCTCAGG
GGGAGCCGACAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNGTGCATGGCTTGCATaAGGTGAATGGCTCACAGCACGCACAGCT
TGCAGAGGATGCACCCTACAGCTCACACAaGACAtACAGCTCgCCAGATCTGTGCTGTTC
ACGTGCATCCCATGCATTCCCTATGAGCCCTGtGTGCTGTGCGTAGCTTGTAGGGTGTTC
CAGGCTTGCAtGGGGTGCACGGCTCACGGGGGCCGCACAGCTCACATCGGGTGCAGGACT
CACACAGCCCCCCCCAGGCAGCACACGGCtCTGCAGCCCCCCCAGCTCACCCATCACCTC
GAGGGGCAGCAGGTCCTGCTCATCATCGATGCCAGCCACCACCTCGCAGCGGTACAGCCC
CGCATCGCTGGCGCGGGCGGCGCGCAGCAGCAGCGTCCCGTTGTAGCGGTCGCGGGCGTA
GCCGGGGAGGGACACGCGGCCCTCGTAGGCTTTCACCACCTTCACCACGTTGTCCTTGGC
CACCAGGATGGGGACGTCCTCCCTCTGCCCGCTGGCaGAGCGCACCTTGCTCCATTTGAC
GCGGGGGGGGTCCGGGGGCTCGTTGGGGCCCAACGAGGCGGAGGGATGCAGCAGGAAGAG
GCAGGGCAGTGCCACGGGCTCCCCCAGCCCCACTCGCACTGCCTGGTGCTGCACCCGGCT
GATGTGGATCACCTTCCC
pos on source: 4197-5054
Source
File: sources/Gene5.fas
name: Gene5
species: chicken
Primer1
oligo: OL04-689
seq: CCACTGAACCGTATCCCTCA
Tm: 60.91
Primer2
oligo: OL04-690
seq: GGGAAGGTGATCCACATCAG
Tm: 60.33
Use
seq:
cCAggcaGTGCG*AGTGGGGCTGGGGGAGCCCGTGGCACTGCCCTGCCTCTTCCTGCTGC
ATCCCTCCGCCTCGTTGGGCCCCAACGAGCCCCCGGGaCCCCCCCCGCGTCAAATGG*AG
CAAGGTGCGCTCTGCCAGCGGGCAGA*GGG*AGGACGTCCCCATCCTGGTGGCCAAGGAC
AACGTGGTGAAGGTGGTGAAAGCCTACGAGGGCCGCGTGTCCCTCCCCGGC*TACGCCCG
TGACCGCTACAATGGGACGCTGCTGCTGCGCGCCGCCCGCGCCAGCGATGCGGGGCTGTA
CCGCTGCGAGGTGGTGGCTGGCATCGATGATGAGCAGGACCTGCTGCCCCTcGAGGTGAT
GGGTGAGCTGGGGGGGCTGCAGGGCCGTGTGCTGCCTGGGGGGGGCTGTGTGAGTCCTGC
ACCCGATGTGAGCTGTGCGGCCCCCGTGAGCTGTGCACCCTGTGCAAGCCTGGAACACCC
TACAAGCTACGCACAGCATGCAAGGCTTATAGGGAATGCATGGGATGCACGTGAACAGCA
CAGATCTGGTGAGCTGTGTGTCCTGTGTGAGCTGTAGGGTGCATCCTCtGCAAGCTGTGC
ATGCTGTGAGCCATTCACCTCATGCAAGCCATGCACACCCtACAAGCTGTGCACCCTATG
TGAGCAGTGCTCTCTGTGTGTCCTctGCAAGCTGTGCATGCTGTCGGCTCCCCCTGAGct
gcgcACCCATGCAAGCCGTGCACACCCTACAAGCTGTGCACTGTATGTGAGTTGCGCACC
CTCTGCAat
revcomp: 1
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| snp_Gene5_3_25 | 25 | 803 | 4999 | S | 1 | 0 |
| snp_Gene5_3_133 | 133 | 697 | 4893 | K | 3 | 1 |
| snp_Gene5_3_292 | 292 | 541 | 4737 | R | 2 | 0 |
| snp_Gene5_3_383 | 383 | 450 | 4646 | | | 1 |
| snp_Gene5_3_452 | 452 | | | Y | 3 | 0 |
| snp_Gene5_3_462 | 462 | | 4567 | R | 5 | 1 |
| snp_Gene5_3_499 | 499 | | | Y | 3 | 0 |
| snp_Gene5_3_500 | 500 | | 4529 | | | 1 |
| snp_Gene5_3_503 | 503 | | | R | 2 | 0 |
| snp_Gene5_3_508 | 508 | | | Y | 1 | 0 |
| snp_Gene5_3_550 | 550 | | 4479 | | | 1 |
| snp_Gene5_3_558 | 558 | | 4471 | | | 1 |
| snp_Gene5_3_562 | 562 | | 4466 | | | 1 |
| snp_Gene5_3_601 | 601 | 232 | 4428 | R | 1 | 0 |
| snp_Gene5_3_621 | 621 | 212 | 4408 | | | 1 |
| snp_Gene5_3_775 | 775 | 58 | 4254 | | | 1 |
SNP remarks
| remark |
| snp_Gene5_3_133 | LLNL_ID=jf1008311; also found by LLNL; Gene5_3_697; M; exon; synonymous |
| snp_Gene5_3_383 | only found by LLNL; Gene5_3_450; intron |
| snp_Gene5_3_462 | also found by LLNL; Gene5_3_371; intron |
| snp_Gene5_3_500 | only found by LLNL; Gene5_3_333; intron |
| snp_Gene5_3_550 | also found by LLNL; not found by script; Gene5_3_283; intron |
| snp_Gene5_3_558 | also found by LLNL; not found by script; Gene5_3_275; intron |
| snp_Gene5_3_562 | also found by LLNL; not found by script; Gene5_3_270; intron |
| snp_Gene5_3_621 | only found by LLNL; Gene5_3_212; intron |
| snp_Gene5_3_775 | only found by LLNL; Gene5_3_58; intron |
Samples
Sample meta data
| file |
| sample_1_Gene5-3F_ASP_13F_2774_H06_16.ab1 | 1_Gene5-3F_ASP_13F_2774_H06_16.ab1 |
| sample_1_Gene5-3F_S5_M_8721_A05_01.ab1 | 1_Gene5-3F_S5_M_8721_A05_01.ab1 |
| sample_1_Gene5-3R_ASP_11F_2718_F04_12.ab1 | 1_Gene5-3R_ASP_11F_2718_F04_12.ab1 |
| sample_1_Gene5-3R_ASP_11M_2734_E04_10.ab1 | 1_Gene5-3R_ASP_11M_2734_E04_10.ab1 |
| sample_1_Gene5-3R_ASP_13F_2774_H04_16.ab1 | 1_Gene5-3R_ASP_13F_2774_H04_16.ab1 |
| sample_1_Gene5-3R_ASP_13M_2757_G04_14.ab1 | 1_Gene5-3R_ASP_13M_2757_G04_14.ab1 |
| sample_1_Gene5-3R_C44_F_9040_E03_09.ab1 | 1_Gene5-3R_C44_F_9040_E03_09.ab1 |
| sample_1_Gene5-3R_C44_M_2136_D03_07.ab1 | 1_Gene5-3R_C44_M_2136_D03_07.ab1 |
| sample_1_Gene5-3R_C44_O_2136_F03_11.ab1 | 1_Gene5-3R_C44_O_2136_F03_11.ab1 |
| sample_1_Gene5-3R_RJF_29_H03_15.ab1 | 1_Gene5-3R_RJF_29_H03_15.ab1 |
| sample_1_Gene5-3R_S5_F_6030_B03_03.ab1 | 1_Gene5-3R_S5_F_6030_B03_03.ab1 |
| sample_1_Gene5-3R_S5_M_8721_A03_01.ab1 | 1_Gene5-3R_S5_M_8721_A03_01.ab1 |
| sample_1_Gene5-3R_S5_O_6030_C03_05.ab1 | 1_Gene5-3R_S5_O_6030_C03_05.ab1 |
| sample_1_Gene5-3R_WL_HF_6320_B04_04.ab1 | 1_Gene5-3R_WL_HF_6320_B04_04.ab1 |
| sample_1_Gene5-3R_WL_LM_5260_C04_06.ab1 | 1_Gene5-3R_WL_LM_5260_C04_06.ab1 |
Sample genotyping data
| 25 | 133 | 292 | 383 | 452 | 462 | 499 | 500 | 503 | 508 | 550 | 558 | 562 | 601 | 621 | 775 |
| sample_1_Gene5-3F_ASP_13F_2774_H06_16.ab1 | | | | | C | R | C | | G | C | | | | G | | |
| sample_1_Gene5-3F_S5_M_8721_A05_01.ab1 | | | G | | T | G | T | | A | T | | | | A | | |
| sample_1_Gene5-3R_ASP_11F_2718_F04_12.ab1 | G | T | | | | | | | | | | | | | | |
| sample_1_Gene5-3R_ASP_11M_2734_E04_10.ab1 | | T | | | | | | | | | | | | | | |
| sample_1_Gene5-3R_ASP_13F_2774_H04_16.ab1 | G | T | G | | C | A | | | | | | | | | | |
| sample_1_Gene5-3R_ASP_13M_2757_G04_14.ab1 | G | K | A | | | | | | | | | | | | | |
| sample_1_Gene5-3R_C44_F_9040_E03_09.ab1 | G | T | | | | | | | | | | | | | | |
| sample_1_Gene5-3R_C44_M_2136_D03_07.ab1 | G | T | G | | | | | | | | | | | | | |
| sample_1_Gene5-3R_C44_O_2136_F03_11.ab1 | | T | | | | | | | | | | | | | | |
| sample_1_Gene5-3R_RJF_29_H03_15.ab1 | G | T | G | | C | G | | | | | | | | | | |
| sample_1_Gene5-3R_S5_F_6030_B03_03.ab1 | S | T | G | | | | | | | | | | | | | |
| sample_1_Gene5-3R_S5_M_8721_A03_01.ab1 | G | T | G | | | | | | | | | | | | | |
| sample_1_Gene5-3R_S5_O_6030_C03_05.ab1 | G | T | G | | | | | | | | | | | | | |
| sample_1_Gene5-3R_WL_HF_6320_B04_04.ab1 | | T | | | | | | | | | | | | | | |
| sample_1_Gene5-3R_WL_LM_5260_C04_06.ab1 | G | T | G | | | | | | | | | | | | | |
PCR ID: Gene6_1
Projects: LLNL reseq SNPs
Researchers: Jan Aerts
Design
seq:
TCCTTCACCTGTTGTAGGGCTCAGCCACAGCTCTGTTCCATTACTGGGAAGGTGACTCCA
TGGCCCAGCACgCAGCGGCTGTGCCACCCTCAGGGCTGGCTGTGCCCTCGCAGTGCCGGC
TCAGGACTGGGGCCATACgTACAGCCCATGGTGCTGGCAGCTCCCACCCTCCAGCGCAGG
CACAGGGCGCTGCTCCTCAGCACTGCACCACGTTCATGGGCTCTGCATGCCTGCAGTGCT
GCATCAGCAGCGGGGAGGTGGGGGGGGACCATGGCCTCAGTCCACGCTGCTGCTGGGGAG
CGGGGCTGGGAGTGGCGTGGGATGGACGGCACCAAGCAGAGGGTCACCCACTGCTCTATG
TGCCCACAGAGCCCCTTCCACTTCCACATGGACCGGCAGAGCTCTCTGGAGAtGCTGGCA
GAGGTGCTGGCGAGCATCCTGCAGGCCCACGAGTGGCGCGAGGCCACGCTGGTGCTGTGC
CGCCCCTGGGATGTCACCGCCTTCCTCGACCATGCACAGCTCTCCCTGCACACTGTGCTG
GACCTCCGCTGCCTGCATGAGCCCAGGGCTGAGCGGTGCCTCCGGCAGCACCGGGAGCAC
CTGGGTGCCCTCTCTGGCCCTGTGCTGGTGCTGGGCTGCGACCTGCGGCGCGCACGGCGG
CTCTTCAGGGCGGCGGAGCGTGCGGGGCTGCGGGCGCAGGACGTGCGCTGGGTGCTGGGC
TCCCCACTGCACGCCGCCGAGCTGCAGGGCGAGGATCTGCCCATGGGGCTGCTGGCCTTT
GGGGAGGTGGGCGCCaCGCCGCTGGAGGCCGTTGTGCGTGATGCAGTGGAGTTGGTG
pos on source: 89-925
Source
File: sources/Gene6.fas
name: Gene6
species: chicken
Primer1
oligo: OL04-691
seq: TCCTTCACCTGTTGTAGGGC
Tm: 60.11
Primer2
oligo: OL04-692
seq: CACCAACTCCACTGCATCAC
Tm: 60.16
Use
seq: unknown
revcomp: 0
SNPs
| pos | pos_design | pos_source | amb | rank | remarks? |
| Gene6_1_72 | 72 | | | | | 1 |
| Gene6_1_139 | 139 | | | | | 1 |
| Gene6_1_413 | 413 | | | Y | | 1 |
| Gene6_1_796 | 796 | | | R | | 1 |
SNP remarks
| remark |
| Gene6_1_72 | intron |
| Gene6_1_139 | intron |
| Gene6_1_413 | exon; non-synonymous |
| Gene6_1_796 | exon; non-synonymous |
Samples
No samples