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 |
|---|---|---|---|---|---|---|
| A13 F69 I0 R1 | 1426 | 148.0 | 5875178 | 97.4% | 5722423 | 123.7 |
Breseq alignment
| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NC_000913 | 120,154 | Δ1 bp | 17.5% | intergenic (+19/+24) | ampE → / ← aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 120,154 | 0 | T | . | 17.5% | 200.5 / 38.1 | 63 | intergenic (+19/+24) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| Reads supporting (aligned to +/- strand): ref base T (25/27); new base . (6/5); total (31/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.50e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01 | |||||||||||
TCTGGCGCGTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGTCATCAGCATAATCAC > NC_000913/120009‑120300 | tctGGCGCGTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTa < 1:829320/149‑1 (MQ=255) gcgcGTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑ggg > 3:147047/1‑149 (MQ=255) gcgTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTg < 2:617309/149‑1 (MQ=255) cgTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTTGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 4:1277710/149‑1 (MQ=255) gTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa > 4:870272/1‑148 (MQ=255) gTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 3:870272/148‑1 (MQ=255) tGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCCCTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAg < 2:959703/148‑1 (MQ=255) tGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAg > 1:959703/1‑148 (MQ=255) gAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑gg < 1:980945/142‑1 (MQ=255) gAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑gg > 2:980945/1‑142 (MQ=255) aTGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 4:212685/139‑1 (MQ=255) aTGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa > 3:212685/1‑139 (MQ=255) gTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGt < 2:679847/129‑1 (MQ=255) gTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGt > 1:679847/1‑129 (MQ=255) tCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 1:641070/136‑1 (MQ=255) tCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa > 2:641070/1‑136 (MQ=255) cAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTtctc < 4:147047/149‑1 (MQ=255) aagaaAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACa > 4:55818/1‑149 (MQ=255) aaaaCCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGtt > 1:11854/1‑133 (MQ=255) aaaaCCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGtt < 2:11854/133‑1 (MQ=255) aCCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGc < 3:55818/149‑1 (MQ=255) ccTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGAt > 1:1330439/1‑102 (MQ=255) ccTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGAt > 1:1186338/1‑102 (MQ=255) ccTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGAt < 2:1186338/102‑1 (MQ=255) ccTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGAt < 2:1330439/102‑1 (MQ=255) cTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCg > 2:193009/1‑149 (MQ=255) gtggtcgtggtGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTaa < 2:302512/97‑1 (MQ=255) gtggtcgtggtGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTaa > 1:302512/1‑97 (MQ=255) ggtggtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATc < 4:1245974/149‑1 (MQ=255) tggtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAg > 2:529664/1‑149 (MQ=255) gtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 1:586900/68‑1 (MQ=255) gtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa < 1:740031/68‑1 (MQ=255) gtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa > 2:586900/1‑68 (MQ=255) gtgATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGa > 2:740031/1‑68 (MQ=255) actGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATc < 1:193009/149‑1 (MQ=255) aCGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTg < 3:708205/52‑1 (MQ=255) aCGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTg > 4:708205/1‑52 (MQ=255) aCGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGt < 1:529664/149‑1 (MQ=255) aTTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAg > 4:545580/1‑51 (MQ=255) aTTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAg < 3:545580/51‑1 (MQ=255) gCCCTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAg > 4:3894/1‑115 (MQ=255) gCCCTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAg < 3:3894/115‑1 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGt < 1:149439/59‑1 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGt > 2:149439/1‑59 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATccc < 2:1060433/105‑1 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGaaa < 2:1033763/124‑1 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGaaa > 1:1033763/1‑124 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTgg < 1:957126/137‑1 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTgg > 2:957126/1‑137 (MQ=255) ccTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTCTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCAAACACGATCAGCCATAcc > 1:1060433/1‑105 (MQ=255) ccTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTggg < 1:409875/138‑1 (MQ=255) ccTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTggg > 2:409875/1‑138 (MQ=255) ccTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTgg < 2:1109275/137‑1 (MQ=255) ccTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTgg > 1:1109275/1‑137 (MQ=255) cTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGTCATCAGCATa > 1:465916/1‑149 (MQ=255) cTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATTAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGTCATCAGCATa > 2:1359547/1‑149 (MQ=255) cTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAgg < 1:779075/113‑1 (MQ=255) cTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAgg > 2:779075/1‑113 (MQ=255) cTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGtata < 3:130480/117‑1 (MQ=255) cTCACCC‑GTACAGGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGtata > 4:130480/1‑117 (MQ=255) ccTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGtcatca > 3:478305/1‑139 (MQ=255) ccTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGtcatca < 4:478305/139‑1 (MQ=255) ccTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGTCATCAGCATAATCAc > 2:1280515/1‑149 (MQ=255) | TCTGGCGCGTGAACCGCATGTCGATAAGGTGGAGACGCCGAAGGCAGCGGTTTCAATGGCGAAGAAAACCTCGTTCGTGGTCGTGGTGGTGATTGCACTACTGACGATTTACGGGGCGTTGGTGTAAAGATTATTGCCCTCACCCTGTAC‑GGGTGAGGGCGTAGAGAGATTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAACAGATAGCCGATACCTAACACGATCAGCCATACCGGGATCAGGTATACCGAAATCGCCATTCCTGGGGTCATCAGCATAATCAC > NC_000913/120009‑120300 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |