ChickenSD
1.General Information
| Reference SNP ID: |
ggaS11663131 |
| Chromosome: |
chr3 |
| Position: |
13 |
| RefSNP Alleles
| G/A |
| NCBI ss link |
|
2.Gene information
| Var ID |
Gene ID |
Transcript ID |
Gene Symbol |
Variant Effect |
Biotype |
cDNA Position |
Allele Change |
Protein ID |
Protein Position |
Residue Change |
| ggaS11663131 |
-
|
-
|
|
intergenic_variant |
- |
0 |
-
=> -
|
- |
0 |
-
=> -
|
3.Individual Genotype
| Individual |
Genotype |
|
101S_L1_I028
|
G
|
|
102S_L3_I037
|
G
|
|
106S_L6_I030
|
G
|
|
107S_L2_I031
|
G
|
|
108S_L6_I032
|
G
|
|
113S_L1_I036
|
G
|
|
114S_L3_I037
|
G
|
|
11S
|
G
|
|
124S_L2_I048
|
G
|
|
128S_L1_I042
|
G
|
|
130S_L4_I044
|
G
|
|
132S_L2_I046
|
G
|
|
134S_L2_I047
|
G
|
|
14S_L2_I021
|
G
|
|
18833
|
G
|
|
24S_L4_I031
|
G
|
|
29S_L3_I036
|
G
|
|
30S_L2_I037
|
G
|
|
35S_L5_I041
|
G
|
|
36S_L5_I042
|
G
|
|
38S_L6_I044
|
G
|
|
39S_L6_I053
|
G
|
|
45S_L2_I002
|
G
|
|
46S_L4_I003
|
G
|
|
47S_L3_I046
|
G
|
|
4S_L4_I004
|
G
|
|
52S_L2_I050
|
G
|
|
53S_L2_I006
|
G
|
|
55S_L1_I008
|
G
|
|
56S_L1_I010
|
G
|
|
63S_L5_I056
|
G
|
|
66S_L2_I003
|
G
|
|
67S_L1_I011
|
G
|
|
68S_L3_I012
|
G
|
|
71S_L3_I023
|
G
|
|
73S_L1_I025
|
G
|
|
74S_L4_I026
|
G
|
|
75S_L3_I027
|
G
|
|
82S
|
G
|
|
83S_L3_I033
|
G
|
|
95S_L8_I025
|
G
|
|
96S_L4_I026
|
G
|
|
98S_L3_I034
|
G
|
|
99S_L2_I035
|
G
|
|
A1
|
G
|
|
A10
|
G
|
|
A12
|
G
|
|
A8
|
G
|
|
BLB1_L2_I007
|
A
|
|
BLO3_L4_I022
|
A
|
|
BYW5_L2_I010
|
A
|
|
GVF
|
A
|
|
India19
|
G
|
|
India27
|
G
|
|
India29
|
G
|
|
India33
|
G
|
|
India55
|
G
|
|
India61
|
G
|
|
India7
|
G
|
|
India9
|
G
|
|
L2
|
G
|
|
N5
|
G
|
|
S-f1_L4_I106
|
G
|
|
S-f2_I107
|
G
|
|
S-m1_I101
|
G
|
|
S-m2_I102
|
G
|
|
SAMN02486156
|
G
|
|
SAMN02486157
|
G
|
|
SAMN02486158
|
G
|
|
SAMN02486159
|
G
|
|
SAMN02486160
|
G
|
|
SAMN02486161
|
G
|
|
SAMN02486166
|
G
|
|
Silkia
|
G
|
|
T2
|
G
|
|
T3
|
G
|
|
T5
|
G
|
|
TD12
|
G
|
|
TD6
|
G
|
|
TD9
|
G
|
|
Tibet
|
G
|
|
Xcelris_10A
|
G
|
|
Xcelris_114
|
G
|
|
Xcelris_11B
|
G
|
|
Xcelris_127
|
G
|
|
Xcelris_128
|
G
|
|
Xcelris_14B
|
G
|
|
Xcelris_176
|
G
|
|
Xcelris_1A
|
G
|
|
Xcelris_1B
|
G
|
|
Xcelris_219
|
G
|
|
Xcelris_227
|
G
|
|
Xcelris_331
|
G
|
|
Xcelris_340
|
G
|
|
Xcelris_379
|
G
|
|
Xcelris_380
|
G
|
|
Xcelris_382
|
G
|
|
Xcelris_385
|
G
|
|
Xcelris_4B
|
G
|
|
Xcelris_5A
|
G
|
|
Xcelris_5B
|
G
|
|
Xcelris_6A
|
G
|
|
Xcelris_6B
|
G
|
|
Xcelris_84
|
G
|
|
Xcelris_8A
|
G
|
|
Y1-f3_L7_I101
|
G
|
|
Y1-m2_L4_I122
|
G
|
|
Y1-m5_L7_I102
|
G
|
|
YPt610
|
G
|
|
YPt641
|
G
|
|
You1
|
G
|
|
Ypt568
|
G
|
|
Ypt571
|
G
|
|
Ypt572
|
G
|
|
Ypt576
|
G
|
|
Ypt578
|
G
|
|
Ypt579
|
G
|
|
Ypt580
|
G
|
|
Ypt581
|
G
|
|
Ypt583
|
G
|
|
Ypt586
|
G
|
|
Ypt587
|
G
|
|
Ypt589
|
G
|
|
Ypt590
|
G
|
|
Ypt593
|
G
|
|
Ypt596
|
G
|
|
Ypt597
|
G
|
|
Ypt598
|
G
|
|
Ypt599
|
G
|
|
Ypt600
|
G
|
|
Ypt606
|
G
|
|
Ypt622
|
G
|
|
Ypt623
|
G
|
|
Ypt626
|
G
|
|
Ypt640
|
G
|
|
Ypt642
|
G
|
|
Ypt643
|
G
|
|
Ypt645
|
G
|
|
Ypt646
|
G
|
|
Ypt647
|
G
|
|
Yt516
|
G
|
|
Yt518
|
G
|
|
Yt520
|
G
|
|
Yt521
|
G
|
|
Yt524
|
G
|
|
Yt526
|
G
|
|
Yt527
|
G
|
|
Yt528
|
G
|
|
Yt529
|
G
|
|
Yt530
|
G
|
|
Yt536
|
G
|
|
Yt538
|
G
|
|
Yt539
|
G
|
|
Yt540
|
G
|
|
india3
|
G
|
|
india49
|
G
|
|
production
|
G
|
|
ypt2063_L6_I005
|
G
|
|
ypt2069_L6_I006
|
G
|
|
ypt2071_L1_I038
|
G
|
|
ypt2100
|
G
|
|
ypt2101
|
G
|
|
ypt2102
|
G
|
|
ypt2103
|
G
|
|
ypt2106
|
G
|
|
ypt2108
|
G
|
|
ypt2109
|
G
|
|
ypt2115
|
G
|
|
ypt2118
|
G
|
|
ypt2119
|
G
|
|
ypt2168
|
G
|
|
ypt2184
|
G
|
|
ypt2187
|
G
|
|
ypt2189
|
G
|
|
ypt2190
|
G
|
|
ypt2200
|
G
|
|
ypt2209
|
G
|
|
ypt2215
|
G
|
|
ypt2220
|
G
|
|
ypt2221
|
G
|
|
ypt2438
|
G
|
|
ypt2439
|
G
|
|
ypt2440
|
G
|
|
ypt2446
|
G
|
|
ypt2447
|
G
|
|
ypt2468
|
G
|
|
ypt2500
|
G
|
|
ypt2512
|
G
|
|
ypt2523
|
G
|
|
ypt2541
|
G
|
|
ypt2544
|
G
|
|
ypt2547
|
G
|
|
ypt2569
|
G
|
|
ypt2601
|
G
|
|
ypt2623
|
G
|
|
ypt2625
|
G
|
|
ypt262_L3_I030
|
G
|
|
ypt2630
|
G
|
|
ypt2638
|
G
|
|
ypt263_L3_I031
|
G
|
|
ypt2650
|
G
|
|
ypt2653
|
G
|
|
ypt2656
|
G
|
|
ypt2661
|
G
|
|
ypt2669
|
G
|
|
ypt2670
|
G
|
|
ypt2672
|
G
|
|
ypt2673
|
G
|
|
ypt2740
|
G
|
|
ypt2760
|
G
|
|
ypt2761
|
G
|
|
ypt2765
|
G
|
|
ypt2781
|
G
|
|
ypt2783
|
G
|
|
ypt2784
|
G
|
|
ypt2785
|
G
|
|
ypt2799
|
G
|
|
ypt2800
|
G
|
|
ypt2822
|
G
|
|
ypt2823
|
G
|
|
ypt2825
|
G
|
|
ypt2826
|
G
|
|
ypt2828
|
G
|
|
ypt2831
|
G
|
|
ypt2832
|
G
|
|
ypt2849
|
G
|
|
ypt2860
|
A
|
|
ypt2887
|
A
|
|
ypt2890_L3_I040
|
A
|
|
ypt2891_L3_I041
|
A
|
|
ypt2909
|
G
|
|
ypt2918
|
G
|
|
ypt2929
|
G
|
|
ypt3001
|
G
|
|
ypt3011
|
G
|
|
ypt3017
|
G
|
|
ypt3028
|
G
|
|
ypt3038
|
G
|
|
ypt3040
|
G
|
|
ypt3046
|
G
|
|
ypt3051
|
G
|
|
ypt3052
|
G
|
|
ypt3072
|
G
|
|
ypt3133
|
G
|
|
ypt3138
|
G
|
|
ypt3139
|
G
|
|
ypt3140
|
G
|
|
ypt3141
|
G
|
|
ypt3142
|
G
|
|
ypt3143
|
G
|
|
ypt3150_L8_I023
|
G
|
|
ypt3160_L8_I024
|
G
|
|
ypt3162_L6_I036
|
G
|
|
ypt3179_L8_I025
|
G
|
|
ypt3180
|
G
|
|
ypt3182_L1_I039
|
G
|
|
ypt3195_L1_I042
|
G
|
|
ypt3196_L2_I043
|
G
|
|
ypt3197_L1_I044
|
G
|
|
ypt3207_L6_I050
|
G
|
|
ypt3213_L8_I029
|
G
|
|
ypt3219_L1_I030
|
G
|
|
ypt3222_L1_I033
|
G
|
|
ypt3224_L8_I043
|
G
|
|
ypt3247_L6_I051
|
G
|
|
ypt3259_L6_I002
|
G
|
|
ypt3260_L6_I003
|
G
|
|
ypt3261_L7_I004
|
G
|
|
ypt3262_L7_I005
|
G
|
|
ypt3274A_L7_I011
|
G
|
|
ypt53_L2_I032
|
G
|
|
ypt898
|
G
|
|
ypt903_L2_I054
|
G
|
|
ypt904_L4_I055
|
G
|
|
ypt906_L3_I001
|
G
|
|
ypt909_L5_I004
|
G
|
|
ypt915
|
G
|
|
ypt917
|
G
|
|
ypt918_L3_I007
|
G
|
|
ypt920_L5_I010
|
G
|
|
ypt921_L8_I011
|
G
|
|
ypt925_L2_I022
|
G
|
|
ypt926_L2_I023
|
G
|
|
ypt943
|
G
|
|
ypt945_L4_I031
|
G
|
|
ypt948_L2_I034
|
G
|
|
ypt953
|
G
|
|
ypt955
|
G
|
|
ypt957
|
G
|
|
ypt961
|
G
|
|
ypt964
|
G
|
|
ypt965
|
G
|
|
ypt973_L4_I037
|
G
|
|
ypt975_L8_I039
|
G
|
|
ypt976_L7_I040
|
G
|
|
ypt977_L2_I041
|
G
|
|
ypt978_L2_I052
|
G
|
|
ypt980_L3_I043
|
G
|
|
ypt984
|
G
|
|
yptwj
|
G
|
|
147830
|
G
|
|
GLF_denovo
|
G
|
|
Ypt4879
|
G
|
4. Population Genetics Analyses
| Population |
Sample # |
Allele:Frequency |
Genotype:Frequency |
|
Afghan |
11 |
G:1.00; A:0.00; |
GG:1.00; |
|
Beijing |
11 |
G:1.00; A:0.00; |
GG:1.00; |
|
Bengal |
15 |
G:0; A:0; |
NN:; |
|
Cornish_UK |
1 |
G:1.00; A:0.00; |
GG:1.00; |
|
Europe_egg |
13 |
G:1.00; A:0.00; |
GG:1.00; |
|
Europe_meat |
4 |
G:1.00; A:0.00; |
GG:1.00; |
|
Gallus_lafayetii |
4 |
G:0; A:0; |
NN:; |
|
Gallus_sonnerattii |
3 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.g.bankiva |
4 |
G:0; A:0; |
NN:; |
|
G.g.gallus |
6 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.g.jabouillei |
27 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.g.murghi |
68 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.g.spadiceus |
36 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.g.spadiceus_Thai |
9 |
G:1.00; A:0.00; |
GG:1.00; |
|
Guangxi |
6 |
G:1.00; A:0.00; |
GG:1.00; |
|
Guangzhou |
6 |
G:1.00; A:0.00; |
GG:1.00; |
|
G.varius |
12 |
G:0.00; A:1.00; |
AA:1.00; |
|
Hainan |
1 |
G:0; A:0; |
NN:; |
|
Henan |
8 |
G:0; A:0; |
NN:; |
|
India |
52 |
G:1.00; A:0.00; |
GG:1.00; |
|
Indonesia |
36 |
G:1.00; A:0.00; |
GG:1.00; |
|
Iran |
182 |
G:1.00; A:0.00; |
GG:1.00; |
|
Jiangsu |
10 |
G:1.00; A:0.00; |
GG:1.00; |
|
Jiangxi |
30 |
G:1.00; A:0.00; |
GG:1.00; |
|
Liaoning |
8 |
G:1.00; A:0.00; |
GG:1.00; |
|
Pakistan |
37 |
G:1.00; A:0.00; |
GG:1.00; |
|
Rhode_USA |
1 |
G:1.00; A:0.00; |
GG:1.00; |
|
Shandong |
18 |
G:1.00; A:0.00; |
GG:1.00; |
|
Shanxi |
8 |
G:1.00; A:0.00; |
GG:1.00; |
|
Srilanka |
7 |
G:0; A:0; |
NN:; |
|
Taiwan |
1 |
G:1.00; A:0.00; |
GG:1.00; |
|
Thailand |
6 |
G:1.00; A:0.00; |
GG:1.00; |
|
Tibet |
113 |
G:1.00; A:0.00; |
GG:1.00; |
|
Vietnan |
7 |
G:1.00; A:0.00; |
GG:1.00; |
|
WhitePlymouth_USA |
1 |
G:0; A:0; |
NN:; |
|
Xinjiang |
30 |
G:1.00; A:0.00; |
GG:1.00; |
|
Yuanbao |
24 |
G:1.00; A:0.00; |
GG:1.00; |
|
Yunnan |
49 |
G:1.00; A:0.00; |
GG:1.00; |
5. Genotype-Phenotype Information
| Chr |
Position |
RSID |
Species/Population |
Trait |
Effect Allele |
P-value |
Reported Gene(s) Symbol |
PMID |
