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 |
|---|---|---|---|---|---|---|
| A4 F1 I2 R1 | 780 | 68.3 | 3343050 | 93.5% | 3125751 | 102.9 |
Breseq alignment
| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 1,042,775 | C→T | R479H (CGC→CAC) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,042,775 | 0 | C | T | 100.0% | 168.6 / NA | 52 | R479H (CGC→CAC) | etk | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (25/27); total (25/27) | |||||||||||
GTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGCC > NC_000913/1042652‑1042908 | gTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg > 2:966849/1‑134 (MQ=255)gTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg < 1:966849/134‑1 (MQ=255) cacaGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGc < 1:1079353/112‑1 (MQ=255) cacaGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGc > 2:1079353/1‑112 (MQ=255) cagAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCa < 2:1567588/105‑1 (MQ=255) cagAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCa > 1:1567588/1‑105 (MQ=255) ccgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg < 2:486587/139‑1 (MQ=255) cgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc > 2:21274/1‑139 (MQ=255) cgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc < 1:21274/139‑1 (MQ=255) gTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCAGCTGATTAGAAAATAAATTTTTCATACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct < 1:533933/139‑1 (MQ=255) ggAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg > 1:743319/1‑79 (MQ=255) ggAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg < 2:743319/79‑1 (MQ=255) gggATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCtt > 1:310064/1‑139 (MQ=255) aGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGAc > 1:320011/1‑73 (MQ=255) aGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGAc < 2:320011/73‑1 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGa < 1:89761/65‑1 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGa > 2:89761/1‑65 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGTCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACa > 1:1142988/1‑139 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg < 1:877059/98‑1 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg > 2:877059/1‑98 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc < 2:1111163/99‑1 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc > 1:1111163/1‑99 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg < 1:502121/116‑1 (MQ=255) tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg > 2:502121/1‑116 (MQ=255) ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg < 2:171130/108‑1 (MQ=255) ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg > 1:171130/1‑108 (MQ=255) aTTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGcc > 2:1024948/1‑139 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACt > 2:1336638/1‑43 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACt < 1:1336638/43‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACa > 2:613865/1‑49 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACa < 1:613865/49‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGa > 1:1571664/1‑55 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGa < 2:1571664/55‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGTCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACgg < 2:1142988/139‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct > 2:368276/1‑84 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct < 1:368276/84‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg < 1:1391979/98‑1 (MQ=255) aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg > 2:1391979/1‑98 (MQ=255) ataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGc < 2:310064/139‑1 (MQ=255) aaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg < 1:594413/95‑1 (MQ=255) aaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg > 2:594413/1‑95 (MQ=255) tttCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa > 1:817551/1‑118 (MQ=255) tttCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa < 2:817551/118‑1 (MQ=255) ttACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAACACGGc > 1:1351083/1‑128 (MQ=255) ttACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAACACGGc < 2:1351083/128‑1 (MQ=255) aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCca > 1:1204331/1‑125 (MQ=255) aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCca < 2:1204331/125‑1 (MQ=255) aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAAc < 2:857862/136‑1 (MQ=255) aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAAc > 1:857862/1‑136 (MQ=255) cGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGc > 2:1507269/1‑139 (MQ=255) gggTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGcc < 1:1507269/139‑1 (MQ=255) gggTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGcc < 1:1024948/139‑1 (MQ=255) | GTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGCC > NC_000913/1042652‑1042908 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |