| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 30.6% | 53.5 / 32.9 | 49 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base C (17/17); new base T (5/10); total (22/27) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.58e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.04e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCT > NC_000913_3_pae_pgi/4295182‑4295468 | gCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGCTTTTGTAGGTCGAATAACGCGTTTACGC‑CGCATCCGCCATCAATGCCTGATGCg > 1:188741/1‑149 (MQ=11)gCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCg > 1:25413/1‑149 (MQ=32) gTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGAc > 1:381261/1‑149 (MQ=17) aTGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTATTAGCAGGCCTACGCCAAACAGCGCAATAGCCTGAGTTAACGTGGTTTTGTAGGTCGGCAAAGGCATTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCtt > 2:346555/1‑149 (MQ=11) gCCGGATCCGACATCAACGCCTGATGCGACGCTTACCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGc < 1:5290/149‑1 (MQ=255) cGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCcg > 1:160468/1‑149 (MQ=25) gCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCcgc < 2:160468/149‑1 (MQ=21) cATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCcgcg < 2:279236/149‑1 (MQ=25) tCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGGCGCTTGCCGTGTc > 1:367204/1‑149 (MQ=255) tCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAg < 1:176437/149‑1 (MQ=21) caaagtcTGATGAGACGATTGCCGCGTCTTATCAGCGCTACGCCAGACAGCGCAATGGTCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCACCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAgg < 2:466641/143‑1 (MQ=11) aaCGACTGATGTGACGCCTTGCGCGTCTTATCAGGCCTACGCCAGACAGCGCATTAGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGc < 2:407469/149‑1 (MQ=11) aCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGcc < 2:302587/149‑1 (MQ=21) aCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGcc > 2:475054/1‑149 (MQ=21) gCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTa > 1:433816/1‑149 (MQ=38) ccTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAc < 1:398788/149‑1 (MQ=18) cTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTatc < 2:381261/149‑3 (MQ=17) cTGACGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGGGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACg < 2:170751/149‑1 (MQ=255) gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCa < 1:281165/134‑1 (MQ=21) gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCa > 2:281165/1‑134 (MQ=38) cGCTTAACGCGTCTTATCAGGCCGACGCCAGACAGCCCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAgc < 1:224619/149‑1 (MQ=255) cgcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGcc < 2:167882/114‑1 (MQ=37) cgcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGAAAGCCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCGTGATGCGCCGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAg > 2:275993/1‑149 (MQ=11) cTTACCAGGCCTACGCAAGACAGCGCAATGGCCTGATTTCGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGa < 2:4050/149‑1 (MQ=255) tATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCt < 1:484122/92‑1 (MQ=21) tATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCt > 2:484122/1‑92 (MQ=34) gCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGCCACCGCAATAGCCCGATTTcgcgg > 2:208860/1‑148 (MQ=11) tccggtgttAGCGCGATTTGTTGGGCCGTATCAGGCGTATCCCC‑CGCATCATACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGc < 2:338920/142‑1 (MQ=11) aGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGcc < 2:25413/149‑1 (MQ=17) gTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCg < 2:248557/114‑1 (MQ=40) tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAg > 2:473234/1‑78 (MQ=255) tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAg < 1:473234/78‑1 (MQ=255) tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGCCAGCGCAATAGCCTGCTTTAGCGTGATTTTGTAGGTCGGACAACGCGTTTATGCCGCAt > 2:462548/1‑149 (MQ=255) tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGcgt > 1:176736/1‑147 (MQ=39) tCGGATAAGGCGTTTACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTa < 1:84156/71‑1 (MQ=255) tCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTa > 2:84156/1‑71 (MQ=255) ggCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGc > 2:11473/1‑82 (MQ=255) ggCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGc < 1:11473/82‑1 (MQ=255) gTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTGGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGAc > 1:265481/1‑149 (MQ=38) cgttACGCGCGCATCCGTCATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGTCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGCTTATGCCGCATCCGACATCAACGCCTGATGCGa < 2:296896/147‑1 (MQ=11) gttACGC‑CGGATCCGGCGTGAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACg < 2:230870/148‑1 (MQ=255) tACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCt < 1:346555/149‑1 (MQ=37) tCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTc < 2:433816/149‑1 (MQ=34) cAACGCCTGATGCGACGCTTGCCGCGTCTTATCAgg > 1:100028/1‑36 (MQ=40) cAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACg < 2:389212/118‑1 (MQ=33) cAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACg > 1:389212/1‑118 (MQ=33) aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTGACCGCGTCTTTTCAGGc > 1:136906/1‑149 (MQ=12) aCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTaa > 2:286054/1‑133 (MQ=31) aCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTaa < 1:286054/133‑1 (MQ=31) cGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCt > 1:279236/1‑149 (MQ=11) | GCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑CGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCT > NC_000913_3_pae_pgi/4295182‑4295468 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |