Content-Type: text/html; charset=ISO-8859-1 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

pospos_designpos_sourceambrankremarks?
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_110exon; non-synonymous
Gene1_1_273intron
Gene1_1_315intron
Gene1_1_319intron
Gene1_1_329intron
Gene1_1_340intron
Gene1_1_350intron
Gene1_1_400intron
Gene1_1_450intron
Gene1_1_555intron
Gene1_1_559intron

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

pospos_designpos_sourceambrankremarks?
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_194LLNL_ID=jf1002729; also found by LLNL; Gene2_1_286; amb M; pos 286 on design; exon; non-synonymous
snp_Gene2_1_214LLNL_ID=jf1002728; also found by LLNL; Gene2_1_266; amb R; pos 266 on design; exon; non-synonymous
snp_Gene2_1_219LLNL_ID=jf1002727; also found by LLNL; Gene2_1_261; amb R; pos 261 on design; exon; synonymous
snp_Gene2_1_397only 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.ab11_Gene2-1F_ASP_11F_2718_F02_12.ab1
sample_1_Gene2-1F_ASP_11M_2734_E02_10.ab11_Gene2-1F_ASP_11M_2734_E02_10.ab1
sample_1_Gene2-1F_ASP_13F_2774_H02_16.ab11_Gene2-1F_ASP_13F_2774_H02_16.ab1
sample_1_Gene2-1F_ASP_13M_2757_G02_14.ab11_Gene2-1F_ASP_13M_2757_G02_14.ab1
sample_1_Gene2-1F_RJF_24_G01_13.ab11_Gene2-1F_RJF_24_G01_13.ab1
sample_1_Gene2-1F_RJF_29_H01_15.ab11_Gene2-1F_RJF_29_H01_15.ab1
sample_1_Gene2-1F_S5_O_6030_C01_05.ab11_Gene2-1F_S5_O_6030_C01_05.ab1
sample_1_Gene2-1F_WL_HF_6144_A02_02.ab11_Gene2-1F_WL_HF_6144_A02_02.ab1
sample_1_Gene2-1F_WL_LF_7330_D02_08.ab11_Gene2-1F_WL_LF_7330_D02_08.ab1
sample_1_Gene2-1F_WL_LM_5260_C02_06.ab11_Gene2-1F_WL_LM_5260_C02_06.ab1
sample_1_Gene2-1R_ASP_11F_2718_F02_12.ab11_Gene2-1R_ASP_11F_2718_F02_12.ab1
sample_1_Gene2-1R_ASP_11M_2734_E02_10.ab11_Gene2-1R_ASP_11M_2734_E02_10.ab1
sample_1_Gene2-1R_ASP_13F_2774_H02_16.ab11_Gene2-1R_ASP_13F_2774_H02_16.ab1
sample_1_Gene2-1R_ASP_13M_2757_G02_14.ab11_Gene2-1R_ASP_13M_2757_G02_14.ab1
sample_1_Gene2-1R_C44_F_9040_E01_09.ab11_Gene2-1R_C44_F_9040_E01_09.ab1
sample_1_Gene2-1R_C44_M_2136_D01_07.ab11_Gene2-1R_C44_M_2136_D01_07.ab1
sample_1_Gene2-1R_C44_O_2136_F01_11.ab11_Gene2-1R_C44_O_2136_F01_11.ab1
sample_1_Gene2-1R_RJF_24_G01_13.ab11_Gene2-1R_RJF_24_G01_13.ab1
sample_1_Gene2-1R_S5_F_6030_B01_03.ab11_Gene2-1R_S5_F_6030_B01_03.ab1
sample_1_Gene2-1R_S5_M_8721_A01_01.ab11_Gene2-1R_S5_M_8721_A01_01.ab1
sample_1_Gene2-1R_S5_O_6030_C01_05.ab11_Gene2-1R_S5_O_6030_C01_05.ab1
sample_1_Gene2-1R_WL_HF_6144_A02_02.ab11_Gene2-1R_WL_HF_6144_A02_02.ab1
sample_1_Gene2-1R_WL_HF_6320_B02_04.ab11_Gene2-1R_WL_HF_6320_B02_04.ab1
sample_1_Gene2-1R_WL_LF_7330_D02_08.ab11_Gene2-1R_WL_LF_7330_D02_08.ab1
sample_1_Gene2-1R_WL_LM_5260_C02_06.ab11_Gene2-1R_WL_LM_5260_C02_06.ab1

Sample genotyping data
147194204207214215219361371397
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

pospos_designpos_sourceambrankremarks?
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_-2only found by LLNL; Gene2_2_884; intron
snp_Gene2_2_391LLNL_ID=jf1002734; Gene2_2_492; also found by LLNL; exon; synonymous; amb Y
snp_Gene2_2_772also found by LLNL; Gene2_2_116; intron
snp_Gene2_2_814also found by LLNL; Gene2_2_75; intron

Samples

Sample meta data
file
sample_1_Gene2-2F_ASP_11F_2718_F04_12.ab11_Gene2-2F_ASP_11F_2718_F04_12.ab1
sample_1_Gene2-2F_ASP_11M_2734_E04_10.ab11_Gene2-2F_ASP_11M_2734_E04_10.ab1
sample_1_Gene2-2F_ASP_13F_2774_H04_16.ab11_Gene2-2F_ASP_13F_2774_H04_16.ab1
sample_1_Gene2-2F_C44_F_9040_E03_09.ab11_Gene2-2F_C44_F_9040_E03_09.ab1
sample_1_Gene2-2F_C44_M_2136_D03_07.ab11_Gene2-2F_C44_M_2136_D03_07.ab1
sample_1_Gene2-2F_C44_O_2136_F03_11.ab11_Gene2-2F_C44_O_2136_F03_11.ab1
sample_1_Gene2-2F_RJF_24_G03_13.ab11_Gene2-2F_RJF_24_G03_13.ab1
sample_1_Gene2-2F_RJF_29_H03_15.ab11_Gene2-2F_RJF_29_H03_15.ab1
sample_1_Gene2-2F_S5_F_6030_B03_03.ab11_Gene2-2F_S5_F_6030_B03_03.ab1
sample_1_Gene2-2F_S5_M_8721_A03_01.ab11_Gene2-2F_S5_M_8721_A03_01.ab1
sample_1_Gene2-2F_S5_O_6030_C03_05.ab11_Gene2-2F_S5_O_6030_C03_05.ab1
sample_1_Gene2-2F_WL_HF_6144_A04_02.ab11_Gene2-2F_WL_HF_6144_A04_02.ab1
sample_1_Gene2-2F_WL_HF_6320_B04_04.ab11_Gene2-2F_WL_HF_6320_B04_04.ab1
sample_1_Gene2-2F_WL_LF_7330_D04_08.ab11_Gene2-2F_WL_LF_7330_D04_08.ab1
sample_1_Gene2-2F_WL_LM_5260_C04_06.ab11_Gene2-2F_WL_LM_5260_C04_06.ab1
sample_1_Gene2-2R_ASP_11F_2718_F02_12.ab11_Gene2-2R_ASP_11F_2718_F02_12.ab1
sample_1_Gene2-2R_ASP_11M_2734_E02_10.ab11_Gene2-2R_ASP_11M_2734_E02_10.ab1
sample_1_Gene2-2R_ASP_13F_2774_H02_16.ab11_Gene2-2R_ASP_13F_2774_H02_16.ab1
sample_1_Gene2-2R_ASP_13M_2757_G02_14.ab11_Gene2-2R_ASP_13M_2757_G02_14.ab1
sample_1_Gene2-2R_C44_F_9040_E01_09.ab11_Gene2-2R_C44_F_9040_E01_09.ab1
sample_1_Gene2-2R_C44_M_2136_D01_07.ab11_Gene2-2R_C44_M_2136_D01_07.ab1
sample_1_Gene2-2R_C44_O_2136_F01_11.ab11_Gene2-2R_C44_O_2136_F01_11.ab1
sample_1_Gene2-2R_RJF_24_G01_13.ab11_Gene2-2R_RJF_24_G01_13.ab1
sample_1_Gene2-2R_RJF_29_H01_15.ab11_Gene2-2R_RJF_29_H01_15.ab1
sample_1_Gene2-2R_S5_F_6030_B01_03.ab11_Gene2-2R_S5_F_6030_B01_03.ab1
sample_1_Gene2-2R_S5_M_8721_A01_01.ab11_Gene2-2R_S5_M_8721_A01_01.ab1
sample_1_Gene2-2R_S5_O_6030_C01_05.ab11_Gene2-2R_S5_O_6030_C01_05.ab1
sample_1_Gene2-2R_WL_HF_6144_A02_02.ab11_Gene2-2R_WL_HF_6144_A02_02.ab1
sample_1_Gene2-2R_WL_HF_6320_B02_04.ab11_Gene2-2R_WL_HF_6320_B02_04.ab1
sample_1_Gene2-2R_WL_LF_7330_D02_08.ab11_Gene2-2R_WL_LF_7330_D02_08.ab1
sample_1_Gene2-2R_WL_LM_5260_C02_06.ab11_Gene2-2R_WL_LM_5260_C02_06.ab1

Sample genotyping data
-2112374767780191376391395416421429432438550583584598599621622624625647727761772814
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

pospos_designpos_sourceambrankremarks?
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_100also found by LLNL; Gene3_1_378; pos 378 on design; intron
snp_Gene3_1_108also found by LLNL; Gene3_1_370; pos 370 on design; intron
snp_Gene3_1_159LLNL_ID=jf1010739; also found by LLNL; Gene3_1_319; amb R; pos 319 on design; exon; synonymous
snp_Gene3_1_197LLNL_ID=jf1010738; only found by LLNL; Gene3_1_282; amb R; pos 282 on design; exon; non-synonymous
snp_Gene3_1_290only found by LLNL; Gene3_1_192; pos 192 on design; intron
snp_Gene3_1_329also found by LLNL; Gene3_1_156; pos 156 on design; intron
snp_Gene3_1_453also 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.ab11_Gene3-1F_ASP_11F_2718_F04_12.ab1
sample_1_Gene3-1F_ASP_11M_2734_E04_10.ab11_Gene3-1F_ASP_11M_2734_E04_10.ab1
sample_1_Gene3-1F_ASP_13F_2774_H04_16.ab11_Gene3-1F_ASP_13F_2774_H04_16.ab1
sample_1_Gene3-1F_ASP_13M_2757_G04_14.ab11_Gene3-1F_ASP_13M_2757_G04_14.ab1
sample_1_Gene3-1F_C44_F_9040_E03_09.ab11_Gene3-1F_C44_F_9040_E03_09.ab1
sample_1_Gene3-1F_C44_M_2136_D03_07.ab11_Gene3-1F_C44_M_2136_D03_07.ab1
sample_1_Gene3-1F_C44_O_2136_F03_11.ab11_Gene3-1F_C44_O_2136_F03_11.ab1
sample_1_Gene3-1F_RJF_24_G03_13.ab11_Gene3-1F_RJF_24_G03_13.ab1
sample_1_Gene3-1F_RJF_29_H03_15.ab11_Gene3-1F_RJF_29_H03_15.ab1
sample_1_Gene3-1F_S5_F_6030_B03_03.ab11_Gene3-1F_S5_F_6030_B03_03.ab1
sample_1_Gene3-1F_S5_M_8721_A03_01.ab11_Gene3-1F_S5_M_8721_A03_01.ab1
sample_1_Gene3-1F_S5_O_6030_C03_05.ab11_Gene3-1F_S5_O_6030_C03_05.ab1
sample_1_Gene3-1F_WL_HF_6144_A04_02.ab11_Gene3-1F_WL_HF_6144_A04_02.ab1
sample_1_Gene3-1F_WL_HF_6320_B04_04.ab11_Gene3-1F_WL_HF_6320_B04_04.ab1
sample_1_Gene3-1F_WL_LF_7330_D04_08.ab11_Gene3-1F_WL_LF_7330_D04_08.ab1
sample_1_Gene3-1F_WL_LM_5260_C04_06.ab11_Gene3-1F_WL_LM_5260_C04_06.ab1
sample_1_Gene3-1R_ASP_11F_2718_F04_12.ab11_Gene3-1R_ASP_11F_2718_F04_12.ab1
sample_1_Gene3-1R_ASP_11M_2734_E04_10.ab11_Gene3-1R_ASP_11M_2734_E04_10.ab1
sample_1_Gene3-1R_ASP_13F_2774_H04_16.ab11_Gene3-1R_ASP_13F_2774_H04_16.ab1
sample_1_Gene3-1R_ASP_13M_2757_G04_14.ab11_Gene3-1R_ASP_13M_2757_G04_14.ab1
sample_1_Gene3-1R_C44_F_9040_E03_09.ab11_Gene3-1R_C44_F_9040_E03_09.ab1
sample_1_Gene3-1R_C44_M_2136_D03_07.ab11_Gene3-1R_C44_M_2136_D03_07.ab1
sample_1_Gene3-1R_C44_O_2136_F03_11.ab11_Gene3-1R_C44_O_2136_F03_11.ab1
sample_1_Gene3-1R_RJF_24_G03_13.ab11_Gene3-1R_RJF_24_G03_13.ab1
sample_1_Gene3-1R_RJF_29_H03_15.ab11_Gene3-1R_RJF_29_H03_15.ab1
sample_1_Gene3-1R_S5_F_6030_B03_03.ab11_Gene3-1R_S5_F_6030_B03_03.ab1
sample_1_Gene3-1R_S5_M_8721_A03_01.ab11_Gene3-1R_S5_M_8721_A03_01.ab1
sample_1_Gene3-1R_S5_O_6030_C03_05.ab11_Gene3-1R_S5_O_6030_C03_05.ab1
sample_1_Gene3-1R_WL_HF_6144_A04_02.ab11_Gene3-1R_WL_HF_6144_A04_02.ab1
sample_1_Gene3-1R_WL_HF_6320_B04_04.ab11_Gene3-1R_WL_HF_6320_B04_04.ab1
sample_1_Gene3-1R_WL_LF_7330_D04_08.ab11_Gene3-1R_WL_LF_7330_D04_08.ab1
sample_1_Gene3-1R_WL_LM_5260_C04_06.ab11_Gene3-1R_WL_LM_5260_C04_06.ab1

Sample genotyping data
100107108158159197199241280290292293294310329435453
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

pospos_designpos_sourceambrankremarks?
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_52LLNL_ID=jf1005911; also found by LLNL; Gene4_1_53; amb W; pos 53 on design; exon; non-synonymous
snp_Gene4_1_148LLNL_ID=jf1005912; also found by LLNL; Gene4_1_147; amb R; pos 147 on design; exon; non-synonymous
snp_Gene4_1_282LLNL_ID=jf1005913; also found by LLNL; Gene4_1_280; amb Y; pos 280 on design; exon; synonymous
snp_Gene4_1_303LLNL_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.ab11_Gene4-1F_ASP_11F_2718_F06_12.ab1
sample_1_Gene4-1F_ASP_11M_2734_E06_10.ab11_Gene4-1F_ASP_11M_2734_E06_10.ab1
sample_1_Gene4-1F_ASP_13F_2774_H06_16.ab11_Gene4-1F_ASP_13F_2774_H06_16.ab1
sample_1_Gene4-1F_C44_F_9040_E05_09.ab11_Gene4-1F_C44_F_9040_E05_09.ab1
sample_1_Gene4-1F_C44_O_2136_F05_11.ab11_Gene4-1F_C44_O_2136_F05_11.ab1
sample_1_Gene4-1F_RJF_24_G05_13.ab11_Gene4-1F_RJF_24_G05_13.ab1
sample_1_Gene4-1F_RJF_29_H05_15.ab11_Gene4-1F_RJF_29_H05_15.ab1
sample_1_Gene4-1F_S5_F_6030_B05_03.ab11_Gene4-1F_S5_F_6030_B05_03.ab1
sample_1_Gene4-1F_S5_M_8721_A05_01.ab11_Gene4-1F_S5_M_8721_A05_01.ab1
sample_1_Gene4-1F_S5_O_6030_C05_05.ab11_Gene4-1F_S5_O_6030_C05_05.ab1
sample_1_Gene4-1F_WL_HF_6144_A06_02.ab11_Gene4-1F_WL_HF_6144_A06_02.ab1
sample_1_Gene4-1F_WL_HF_6320_B06_04.ab11_Gene4-1F_WL_HF_6320_B06_04.ab1
sample_1_Gene4-1F_WL_LF_7330_D06_08.ab11_Gene4-1F_WL_LF_7330_D06_08.ab1
sample_1_Gene4-1F_WL_LM_5260_C06_06.ab11_Gene4-1F_WL_LM_5260_C06_06.ab1
sample_1_Gene4-1R_ASP_11M_2734_E06_10.ab11_Gene4-1R_ASP_11M_2734_E06_10.ab1
sample_1_Gene4-1R_ASP_13F_2774_H06_16.ab11_Gene4-1R_ASP_13F_2774_H06_16.ab1
sample_1_Gene4-1R_ASP_13M_2757_G06_14.ab11_Gene4-1R_ASP_13M_2757_G06_14.ab1
sample_1_Gene4-1R_C44_F_9040_E05_09.ab11_Gene4-1R_C44_F_9040_E05_09.ab1
sample_1_Gene4-1R_C44_M_2136_D05_07.ab11_Gene4-1R_C44_M_2136_D05_07.ab1
sample_1_Gene4-1R_C44_O_2136_F05_11.ab11_Gene4-1R_C44_O_2136_F05_11.ab1
sample_1_Gene4-1R_RJF_24_G05_13.ab11_Gene4-1R_RJF_24_G05_13.ab1
sample_1_Gene4-1R_RJF_29_H05_15.ab11_Gene4-1R_RJF_29_H05_15.ab1
sample_1_Gene4-1R_S5_M_8721_A05_01.ab11_Gene4-1R_S5_M_8721_A05_01.ab1
sample_1_Gene4-1R_S5_O_6030_C05_05.ab11_Gene4-1R_S5_O_6030_C05_05.ab1
sample_1_Gene4-1R_WL_HF_6144_A06_02.ab11_Gene4-1R_WL_HF_6144_A06_02.ab1
sample_1_Gene4-1R_WL_LF_7330_D06_08.ab11_Gene4-1R_WL_LF_7330_D06_08.ab1
sample_1_Gene4-1R_WL_LM_5260_C06_06.ab11_Gene4-1R_WL_LM_5260_C06_06.ab1

Sample genotyping data
52127148175182282303318366
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

pospos_designpos_sourceambrankremarks?
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_66intron
Gene5_1_100exon; synonymous
Gene5_1_164exon; non-synonymous
Gene5_1_172exon; synonymous
Gene5_1_568exon; synonymous
Gene5_1_677exon; non-synonymous
Gene5_1_704exon; 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

pospos_designpos_sourceambrankremarks?
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_111intron
Gene5_2_117intron
Gene5_2_325exon; synonymous
Gene5_2_557exon; synonymous
Gene5_2_587exon; synonymous
Gene5_2_740exon; 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

pospos_designpos_sourceambrankremarks?
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_133LLNL_ID=jf1008311; also found by LLNL; Gene5_3_697; M; exon; synonymous
snp_Gene5_3_383only found by LLNL; Gene5_3_450; intron
snp_Gene5_3_462also found by LLNL; Gene5_3_371; intron
snp_Gene5_3_500only found by LLNL; Gene5_3_333; intron
snp_Gene5_3_550also found by LLNL; not found by script; Gene5_3_283; intron
snp_Gene5_3_558also found by LLNL; not found by script; Gene5_3_275; intron
snp_Gene5_3_562also found by LLNL; not found by script; Gene5_3_270; intron
snp_Gene5_3_621only found by LLNL; Gene5_3_212; intron
snp_Gene5_3_775only found by LLNL; Gene5_3_58; intron

Samples

Sample meta data
file
sample_1_Gene5-3F_ASP_13F_2774_H06_16.ab11_Gene5-3F_ASP_13F_2774_H06_16.ab1
sample_1_Gene5-3F_S5_M_8721_A05_01.ab11_Gene5-3F_S5_M_8721_A05_01.ab1
sample_1_Gene5-3R_ASP_11F_2718_F04_12.ab11_Gene5-3R_ASP_11F_2718_F04_12.ab1
sample_1_Gene5-3R_ASP_11M_2734_E04_10.ab11_Gene5-3R_ASP_11M_2734_E04_10.ab1
sample_1_Gene5-3R_ASP_13F_2774_H04_16.ab11_Gene5-3R_ASP_13F_2774_H04_16.ab1
sample_1_Gene5-3R_ASP_13M_2757_G04_14.ab11_Gene5-3R_ASP_13M_2757_G04_14.ab1
sample_1_Gene5-3R_C44_F_9040_E03_09.ab11_Gene5-3R_C44_F_9040_E03_09.ab1
sample_1_Gene5-3R_C44_M_2136_D03_07.ab11_Gene5-3R_C44_M_2136_D03_07.ab1
sample_1_Gene5-3R_C44_O_2136_F03_11.ab11_Gene5-3R_C44_O_2136_F03_11.ab1
sample_1_Gene5-3R_RJF_29_H03_15.ab11_Gene5-3R_RJF_29_H03_15.ab1
sample_1_Gene5-3R_S5_F_6030_B03_03.ab11_Gene5-3R_S5_F_6030_B03_03.ab1
sample_1_Gene5-3R_S5_M_8721_A03_01.ab11_Gene5-3R_S5_M_8721_A03_01.ab1
sample_1_Gene5-3R_S5_O_6030_C03_05.ab11_Gene5-3R_S5_O_6030_C03_05.ab1
sample_1_Gene5-3R_WL_HF_6320_B04_04.ab11_Gene5-3R_WL_HF_6320_B04_04.ab1
sample_1_Gene5-3R_WL_LM_5260_C04_06.ab11_Gene5-3R_WL_LM_5260_C04_06.ab1

Sample genotyping data
25133292383452462499500503508550558562601621775
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

pospos_designpos_sourceambrankremarks?
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_72intron
Gene6_1_139intron
Gene6_1_413exon; non-synonymous
Gene6_1_796exon; non-synonymous

Samples

No samples