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 |
|---|---|---|---|---|---|---|
| A3 F1 I1 R1 | 781 | 46.9 | 2231650 | 93.5% | 2086592 | 109.0 |
Breseq alignment
| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 3,736,157 | G→A | *393* (TAG→TAA) | xylR → | xylose divergent operon transcriptional activator |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,736,157 | 0 | G | A | 98.0% | 155.0 / ‑5.3 | 49 | *393* (TAG→TAA) | xylR | xylose divergent operon transcriptional activator |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (21/27); minor base C (1/0); total (22/27) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.49e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA > NC_000913/3736022‑3736287 | aaCCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACg‑a < 2:1082960/139‑1 (MQ=255)aaCCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACg‑a > 1:344843/1‑139 (MQ=255) tCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGt < 2:866632/139‑1 (MQ=255) gaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTc < 1:395952/139‑1 (MQ=255) atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTcaca < 2:708385/139‑1 (MQ=255) atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTcaca < 1:515246/139‑1 (MQ=255) cGCAAATTTGCGGTTATCCGTCGCTGCAAGATTTCTACTCAGTTTTTAAAAAAGCATATGACACAACGCCAAAAGAGTATCGCGAAGTACATAGCCATGCCATGTTGTAACCA‑ACGATGATAATTCTCTGCGTcataac > 2:405862/1‑135 (MQ=255) ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg < 2:344843/139‑1 (MQ=255) cATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg < 2:371116/137‑1 (MQ=255) cATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg > 1:371116/1‑137 (MQ=255) cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg > 2:736784/1‑139 (MQ=255) cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg < 2:764916/133‑1 (MQ=255) cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg > 1:764916/1‑133 (MQ=255) aCTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAAc > 2:375753/1‑139 (MQ=255) tctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc < 2:329400/139‑1 (MQ=255) tgttttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTcaca > 1:921758/4‑98 (MQ=255) tgttttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTcaca < 2:921758/95‑1 (MQ=255) ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGcc > 2:499069/1‑139 (MQ=255) aaaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt < 2:294145/139‑1 (MQ=255) aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACg‑aatga < 1:759468/65‑5 (MQ=255) aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACg‑aatga > 2:759468/1‑61 (MQ=255) gacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg > 1:989832/1‑103 (MQ=255) gacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg < 2:989832/103‑1 (MQ=255) cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAAtgatga > 1:191614/1‑54 (MQ=255) cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAAtgatga < 2:191614/54‑1 (MQ=255) gagTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTc > 1:1022826/1‑54 (MQ=255) gagTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTc < 2:1022826/54‑1 (MQ=255) gTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg > 2:846242/1‑76 (MQ=255) gTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg < 1:846242/76‑1 (MQ=255) tATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt > 2:282524/1‑87 (MQ=255) tATCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt < 1:282524/87‑1 (MQ=255) tCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCg > 2:520553/1‑53 (MQ=255) tCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCg < 1:520553/53‑1 (MQ=255) tCGCGATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaac < 1:499069/139‑1 (MQ=255) gcgATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa < 1:318276/139‑1 (MQ=255) gcgATGTAAATAGCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa < 1:736784/139‑1 (MQ=255) gCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaa > 1:104404/1‑114 (MQ=255) gCGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaa < 2:104404/114‑1 (MQ=255) cGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg < 1:828293/73‑1 (MQ=255) cGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg > 2:828293/1‑73 (MQ=255) cGAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCg > 2:226124/1‑139 (MQ=255) gAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAgg > 2:373955/1‑104 (MQ=255) gAGGTCATGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAgg < 1:373955/104‑1 (MQ=255) aTGTTGT‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCa > 2:1080092/1‑139 (MQ=255) tgttgt‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc > 2:29269/1‑75 (MQ=38) tgttgt‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc < 1:29269/75‑1 (MQ=38) tgttgt‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc < 2:683388/94‑1 (MQ=255) tgttgt‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc > 1:683388/1‑94 (MQ=255) tgttgt‑AACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCaa < 1:375753/139‑1 (MQ=255) | AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGT‑AGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAA > NC_000913/3736022‑3736287 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |