| Variant ID: vg0503844364 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844364 |
| Reference Allele: GT | Alternative Allele: GTTT,G,GTT,GTTTT |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TATGCAAGAGGAGGGCCAACTAGTTAATTAATGTGTTTCACCATCACATTATAGATTTCATAAGAGATGTACTAGGATTGTGGGAGTACTTCTCAATTTC[GT/GTTT,G,GTT,GTTTT]
TTTTTTTTAAAAAAAATGCACTTTTGAACATTAACTGTTGTCTTGAGCATAAACATGCAAAATGTGTATAACCAAGAATATATGATCTTCCTAGTAATGG
CCATTACTAGGAAGATCATATATTCTTGGTTATACACATTTTGCATGTTTATGCTCAAGACAACAGTTAATGTTCAAAAGTGCATTTTTTTTAAAAAAAA[AC/AAAC,C,AAC,AAAAC]
GAAATTGAGAAGTACTCCCACAATCCTAGTACATCTCTTATGAAATCTATAATGTGATGGTGAAACACATTAATTAACTAGTTGGCCCTCCTCTTGCATA
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.90% | 9.20% | 0.13% | 0.00% | GTT: 5.52%; GTTT: 0.17%; GTTTT: 0.02% |
| All Indica | 2759 | 98.30% | 0.50% | 0.04% | 0.00% | GTT: 1.20% |
| All Japonica | 1512 | 72.50% | 27.10% | 0.07% | 0.00% | GTT: 0.20%; GTTT: 0.13% |
| Aus | 269 | 15.60% | 0.00% | 1.12% | 0.00% | GTT: 81.41%; GTTT: 1.86% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.00% | 0.00% | GTT: 0.22% |
| Indica III | 913 | 98.20% | 0.40% | 0.11% | 0.00% | GTT: 1.20% |
| Indica Intermediate | 786 | 96.70% | 0.60% | 0.00% | 0.00% | GTT: 2.67% |
| Temperate Japonica | 767 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 34.90% | 64.70% | 0.20% | 0.00% | GTT: 0.20% |
| Japonica Intermediate | 241 | 75.90% | 22.40% | 0.00% | 0.00% | GTT: 0.83%; GTTT: 0.83% |
| VI/Aromatic | 96 | 93.80% | 0.00% | 1.04% | 0.00% | GTT: 3.12%; GTTT: 1.04%; GTTTT: 1.04% |
| Intermediate | 90 | 83.30% | 13.30% | 0.00% | 0.00% | GTT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844364 | GT -> GTTT | LOC_Os05g07260.1 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTT | LOC_Os05g07260.2 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTT | LOC_Os05g07260.4 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTT | LOC_Os05g07260.3 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> G | LOC_Os05g07260.1 | downstream_gene_variant ; 1196.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> G | LOC_Os05g07260.2 | downstream_gene_variant ; 1207.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> G | LOC_Os05g07260.4 | downstream_gene_variant ; 1207.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> G | LOC_Os05g07260.3 | downstream_gene_variant ; 1196.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> G | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTTT | LOC_Os05g07260.1 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTTT | LOC_Os05g07260.2 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTTT | LOC_Os05g07260.4 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTTT | LOC_Os05g07260.3 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTTTT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTT | LOC_Os05g07260.1 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTT | LOC_Os05g07260.2 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTT | LOC_Os05g07260.4 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTT | LOC_Os05g07260.3 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0503844364 | GT -> GTT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.657; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |