| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NZ_CP009273 | 1,799,085 | T→C | pseudogene (1735/1900 nt) | espL1 → | type III secretion system effector EspL1 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,799,085 | 0 | T | C | 96.7% | 209.5 / ‑1.3 | 60 | pseudogene (1735/1900 nt) | espL1 | type III secretion system effector EspL1 |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (28/30); total (29/31) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 | |||||||||||
ATTTATTAAAAGGAGCTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACATCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACATATTATGCTGCTATTAATGCAATCAGCCAAA > NZ_CP009273/1798952‑1799209 | aTTTATTAAAAGGAGCTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGtt < 2:652577/139‑1 (MQ=255) attaAAAGGAGCTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTAtt > 2:83425/1‑138 (MQ=255) ttaAAAGGAGCTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTa < 1:83425/139‑1 (MQ=255) cTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCa < 2:935732/121‑1 (MQ=255) cTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCa > 1:935732/1‑121 (MQ=255) cTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGc > 1:961916/1‑139 (MQ=255) cTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGc < 1:1267318/139‑1 (MQ=255) cTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGc > 1:849810/1‑139 (MQ=255) gCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTa < 2:849810/139‑1 (MQ=255) caGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTaaa > 2:714870/1‑138 (MQ=255) ggAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTAt > 2:772704/1‑115 (MQ=255) ggAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTAt < 1:772704/115‑1 (MQ=255) aaCCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCAt > 1:1107805/1‑139 (MQ=255) cccTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGac < 2:1176226/139‑1 (MQ=255) cccTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGac < 1:47971/139‑1 (MQ=255) cccTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGac < 1:1059/139‑1 (MQ=255) cccTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGa > 2:1059/1‑138 (MQ=255) tGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGacaa > 1:757451/1‑138 (MQ=255) taCATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAg < 1:537435/139‑1 (MQ=255) taCATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAg > 2:158167/1‑139 (MQ=255) aTCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTg > 1:218482/1‑139 (MQ=255) tCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGt < 1:761850/139‑1 (MQ=255) cGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTGGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGtt > 2:358427/1‑139 (MQ=255) cGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGtt > 1:820499/1‑139 (MQ=255) cGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGtt > 2:789919/1‑139 (MQ=255) tGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCata > 1:503212/1‑138 (MQ=255) aaGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCa < 1:789919/139‑1 (MQ=255) gggTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCAtt < 2:1003520/139‑1 (MQ=255) ggTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGt > 1:591400/1‑125 (MQ=255) ggTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGt < 2:591400/125‑1 (MQ=255) aGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAg < 1:234864/139‑1 (MQ=255) aGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAg < 2:757451/139‑1 (MQ=255) cgtcgtGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATa < 1:859146/134‑1 (MQ=255) cgtcgtGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATa > 2:859146/1‑134 (MQ=255) gtcgtGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCAt > 2:541014/1‑138 (MQ=255) atatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTg < 2:192184/135‑1 (MQ=255) tatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACATCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGc > 1:1278960/1‑96 (MQ=255) tatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACATCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGc < 2:1278960/96‑1 (MQ=255) tatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGac < 1:912706/85‑1 (MQ=255) tatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGac > 2:912706/1‑85 (MQ=255) tatatCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGaa < 2:961916/139‑1 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGtt < 2:477191/49‑1 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGtt > 1:477191/1‑49 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCata < 2:93745/99‑1 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCata > 1:93745/1‑99 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCAt > 1:73615/1‑106 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCAt < 2:73615/106‑1 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACata > 2:382685/1‑139 (MQ=255) cGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACata > 1:428177/1‑139 (MQ=255) gACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACata < 2:503212/138‑1 (MQ=255) aCGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTg < 1:491266/91‑1 (MQ=255) aCGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTg > 2:491266/1‑91 (MQ=255) aCGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACatat > 2:204367/1‑138 (MQ=255) ggTGCTTTTGCAAAAAAACATTCTTTTGGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACATATTAtgct < 1:358427/138‑1 (MQ=255) ggTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACATATTAtgct < 2:218482/138‑1 (MQ=255) gTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAg > 2:942320/1‑107 (MQ=255) gTGCTTTTGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAg < 1:942320/107‑1 (MQ=255) ttttGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGaa > 2:82301/1‑121 (MQ=255) ttttGCAAAAAAACATTCTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGaa < 1:82301/121‑1 (MQ=255) cTTTTAGTCAACACCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACATATTATGCTGCTATTAATGCAATCAGCCaaa < 1:714870/138‑1 (MQ=255) | ATTTATTAAAAGGAGCTACAGCACAGGGAACCCCTGCATTATACATCGCCATGAGCAAGGGTAATGAAGACGTCGTGTTATCTTATATATCGACGCTGGGTGCTTTTGCAAAAAAACATTCTTTTAGTCAACATCAGTTATTTACACTATTGGCCGCTAAAAATCATGACAACATGTCAGCTGTTCATATAGCCATTCATCATAAGCATTATAAAACTGTAGAAACATATTATGCTGCTATTAATGCAATCAGCCAAA > NZ_CP009273/1798952‑1799209 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |