Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate | Predicted Mutations | Mean Coverage | Total Reads | Percent Mapped | Mapped Reads | Average Read Length |
|---|---|---|---|---|---|---|
| A9 F1 I1 R1 | 64 | 69.7 | 3300380 | 93.4% | 3082554 | 111.2 |
Breseq alignment
| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 2,227,340 | (C)6→7 | pseudogene (1270/1287 nt) | mdtQ ← | pseudogene, putative channel/filament proteins |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,227,334 | 1 | . | C | 89.9% | 233.3 / 16.7 | 69 | pseudogene (1276/1287 nt) | mdtQ | pseudogene, putative channel/filament proteins |
| Reads supporting (aligned to +/- strand): ref base . (3/4); new base C (34/28); total (37/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.96e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.76e-01 | |||||||||||
CCTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGC > NC_000913/2227195‑2227454 | ccTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAA‑GCGCATATCATCAGCGTTTGTa < 1:1582107/139‑1 (MQ=255) ctgctgCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTa < 2:780584/139‑1 (MQ=255) gctgcGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑cc > 2:390991/1‑139 (MQ=255) gctgcGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑cc < 2:208454/139‑1 (MQ=255) gcgcCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑ccccc < 1:1326070/139‑1 (MQ=255) taataaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCa < 2:617161/139‑1 (MQ=255) taataaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCa < 2:282896/139‑1 (MQ=255) aaCGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGc > 2:1162018/1‑139 (MQ=255) cACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGt < 2:929952/139‑1 (MQ=255) cACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGt > 1:1572239/1‑139 (MQ=255) tttGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGtt > 2:648893/1‑139 (MQ=255) cGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATgg < 2:457508/139‑1 (MQ=255) tCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAg > 1:1256393/1‑139 (MQ=255) tCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAgg > 2:887101/1‑139 (MQ=255) gAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATc < 1:345436/139‑1 (MQ=255) gAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATc < 2:602437/139‑1 (MQ=255) cGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc < 1:887101/139‑1 (MQ=255) ggTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc < 1:147293/139‑1 (MQ=255) ggTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc < 1:1184281/139‑1 (MQ=255) taatCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGc < 1:1162018/139‑1 (MQ=255) tCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAAc < 2:1212595/94‑1 (MQ=255) tCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAAc > 1:1212595/1‑94 (MQ=255) aaCCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGccc < 2:506121/128‑1 (MQ=255) aaCCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGccc > 1:506121/1‑128 (MQ=255) aaCCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACa < 2:1256393/139‑1 (MQ=255) gtgCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCaa < 1:70911/84‑1 (MQ=255) gtgCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCaa > 2:70911/1‑84 (MQ=255) gAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCg > 1:468627/1‑139 (MQ=255) aGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCACATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa < 1:808608/82‑1 (MQ=255) aGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCACATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa > 2:808608/1‑82 (MQ=255) ttCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTc > 2:485443/1‑139 (MQ=255) cACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATc > 1:104860/1‑95 (MQ=255) cACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATc < 2:104860/95‑1 (MQ=255) aacgtttatccagcGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCGCGCTCACGCAGcgcg > 2:1104077/14‑139 (MQ=255) aaCGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGcgcg > 2:910826/1‑139 (MQ=255) gCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCgggg > 1:459555/1‑139 (MQ=255) tGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGAt > 1:848274/1‑139 (MQ=255) aTAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa < 2:2944/62‑1 (MQ=255) aTAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCa > 1:2944/1‑62 (MQ=255) aCGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCt > 2:1361358/1‑139 (MQ=255) aCGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCt < 2:1050229/139‑1 (MQ=255) aCGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCt > 1:819003/1‑139 (MQ=255) cGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCa > 1:4804/1‑56 (MQ=255) cGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCa < 2:4804/56‑1 (MQ=255) aaGTATAGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCt > 1:1384794/1‑139 (MQ=255) aGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACg > 2:567072/1‑42 (MQ=255) aGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACg < 1:567072/42‑1 (MQ=255) aGAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGAcgcg < 1:390991/139‑1 (MQ=255) gAAGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCgg > 1:730153/1‑139 (MQ=255) aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATg < 2:533191/57‑1 (MQ=255) aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATg > 1:533191/1‑57 (MQ=255) aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACa > 2:651983/1‑88 (MQ=255) aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACa < 1:651983/88‑1 (MQ=255) aaGGCGCATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCggg < 2:1572239/139‑1 (MQ=255) ggCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc < 2:1566784/73‑1 (MQ=255) ggCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc > 1:1566784/1‑73 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCa < 1:1201548/37‑1 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCa > 2:1201548/1‑37 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTgg > 2:134615/1‑92 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTgg < 1:134615/92‑1 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACg > 1:121163/1‑102 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACg < 2:121163/102‑1 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGAcg < 1:1113316/130‑1 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGAcg > 2:1113316/1‑130 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCa > 2:1095973/1‑139 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCa > 1:846664/1‑139 (MQ=255) gcATATCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCa > 2:1069536/1‑139 (MQ=255) atatCATCAGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGc > 1:80751/1‑139 (MQ=255) caGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc < 1:1222985/62‑1 (MQ=255) caGCGTTTGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGcc > 2:1222985/1‑62 (MQ=255) tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCt < 1:1208428/59‑1 (MQ=255) tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCt > 2:1208428/1‑59 (MQ=255) tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACa > 2:548072/1‑69 (MQ=255) tttGTACCCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACa < 1:548072/69‑1 (MQ=255) | CCTGCTGCGCCAGTAATAACGCGCACTCTTTGCCGATCCCCGAATCGGAGGCGGTAATAATCGCAACCTGTGCCATCGAGTTCTCCACTTAACGCTGAATAAACGTTAAGTATAGAAGGCGCATATCATCAGCGTTTGTA‑CCCCCCGCCCAACGCACCAGTGAGTTGAATGGAGGCATCCAGCCACTGCCCTTGCAATAACAGGCCATTGGCCCGCTCACGCAGCGCGGGGATTCTGGCTTCGCTGACGCGGGAACCAGC > NC_000913/2227195‑2227454 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |