| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,789,594 | 0 | T | . | 23.5% | 41.3 / 11.0 | 17 | intergenic (+26/‑51) | manR_2/manP | Transcriptional regulator ManR/PTS system mannose‑specific EIIBCA component |
| Reads supporting (aligned to +/- strand): ref base T (9/4); new base . (2/2); total (11/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.84e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TACAAAACAAATGATGCAATTAATTGCTAACTTGGATGATGATTCAGTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTGAGCAGGTAGCAAA > USA300TCH1516_ALE/2789454‑2789727 | tACAAAACAAATGATGCAATTAATTGCTAACTTGGATGATGATTCAGTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCt < 2:175371/141‑1 (MQ=255) tgatgCAATTAATTGCTAACTTGGATGATGATTCAGTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTa < 2:163773/141‑1 (MQ=255) cTTGGATGATGATTCAGTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAat > 1:92509/1‑141 (MQ=255) gTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAgatga > 2:20644/1‑141 (MQ=255) ttAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGc < 2:25410/141‑1 (MQ=255) atgatgATAGTTTAAAGCAACAGTTATTTGAATGCTTTCAAGAATAATGGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTAtt < 2:3118/141‑1 (MQ=255) gTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGc > 1:2445/1‑141 (MQ=255) gTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAACTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGc > 1:161032/1‑141 (MQ=255) gCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAGCGGTAATTATTC‑TTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATgg > 2:7788/1‑141 (MQ=255) gCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTC‑TTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATgg > 2:131095/1‑141 (MQ=255) cAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGc < 1:169972/141‑1 (MQ=255) atTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCCCATGCCCAAATGGCATTGCACACACATACATGGCCCAAGaaa > 2:85271/1‑141 (MQ=255) aCTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTg > 2:93207/1‑141 (MQ=255) aGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATGCGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTGAGc > 1:162521/1‑141 (MQ=255) aCGGTACTTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTAATGAAAACTGTAGCTATTACCGCATGCCCCAATGGCATTGCACATACATGTAGGGCTCAAGCAAAGCTTNAACAAGt > 2:168775/1‑141 (MQ=255) aCGGTAATTATTCTTTTTTTTTTTTTTTTTAATACGCTTACAATATATAAAAGGAAATGATTTTATGAAAATTGTAGCTATTACCTCATTCCCAAATGGCATTGCAAATACATATATAGCTCATGAAAAGCTTGCGCAGGt > 2:119237/1‑141 (MQ=255) aaTTATTC‑TTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTGAGCAGGTAGCaaa < 1:131095/141‑1 (MQ=255) aaTTATTC‑TTTTTTTAGTATCGAGAAGACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTGAGCAGGTAGCaaa < 1:7788/141‑1 (MQ=255) | TACAAAACAAATGATGCAATTAATTGCTAACTTGGATGATGATTCAGTGAACCATTTATGTAGTTTAGATGATCATAGTTTAAAGCAACAGTTATTTGAATACTTACAAGAATAATTGCCACTAGTAACGGTAATTATTCTTTTTTTTAGTATCGAGAATACGCTTACAATATAGAAAAGGAGATGATTTTATGAAAATTGTAGCTATTACCTCATGCCCAAATGGCATTGCACATACATATATGGCTCAAGAAAAGCTTGAGCAGGTAGCAAA > USA300TCH1516_ALE/2789454‑2789727 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |