| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 517,732 | 0 | T | C | 28.6% | 20.5 / 15.0 | 28 | intergenic (+5800/‑963) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| Reads supporting (aligned to +/- strand): ref base T (10/10); new base C (4/4); total (14/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATG > USA300TCH1516_ALE/517593‑517865 | cTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTc < 1:102659/141‑1 (MQ=31) aCGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACCCCTGTTTCCAt > 1:93692/1‑141 (MQ=17) aCGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCAt > 1:190911/1‑141 (MQ=32) aaTCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAacac < 2:88890/141‑1 (MQ=32) aaTCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TATGGTTACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAacca > 2:152045/1‑139 (MQ=12) aaTCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCtt < 1:70231/141‑1 (MQ=32) tCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAg < 2:122131/141‑1 (MQ=32) aaaaTAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGTTGACTATAGCAAGGAGGTCACATCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCg < 1:143476/141‑1 (MQ=17) ataaatGTTTTTCGAAGCAAAATCACTTCTACTTACTATCTAGTTTTAAAGGTATAAATGA‑CA‑TCACCCGAAATAGTAACTATAGCAAGGAGGTCACACCTTTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCg < 2:162098/141‑1 (MQ=11) ataaatGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGAATATATCGGGGAGGTGAAAGTGGGCTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCg > 2:162039/1‑141 (MQ=11) cGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATCACGCAAACATACGTTAATCTCCTTAGCGTCGATGGTAGTCGaa < 1:112794/141‑1 (MQ=11) aaatgtcTTTTACTTTCTATCTAGTTTTGAATGTATAAATTACCTTTCAT‑CG‑TCGGTTGACTATAGCGAGGAGGTCACACGTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGt < 2:208503/135‑1 (MQ=11) aCTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGCCGATCGTAGTCGACATTACGTTcggg > 2:94696/1‑138 (MQ=11) ttA‑TATTCAGATG‑TCTGGTGACTATAGCAAGGTGGTCACACCTGTTCCCATGCCGAAGACAGAAGTTAAGCCCCTTAGCGTCGATGGTAGTCGAACTTTCGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcc > 2:109974‑M2/1‑129 (MQ=255) a‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaa < 1:150548‑M2/141‑15 (MQ=255) cATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATACGAt > 1:96624/1‑141 (MQ=17) tatG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCg > 1:106710/1‑141 (MQ=32) tG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggtta < 1:199342‑M2/141‑24 (MQ=255) g‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCAt < 2:39141/141‑1 (MQ=32) cTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTg > 1:185216/1‑141 (MQ=32) tgtGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaa > 1:68489‑M2/2‑113 (MQ=255) ggTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTgag < 1:62844/141‑1 (MQ=32) tGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGAc > 1:58078/1‑141 (MQ=32) gACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataa > 1:102623‑M2/1‑110 (MQ=255) aacTATAGCAAGGAGGTCACACCTGTTCCCATGCCAAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataa > 2:69914‑M2/2‑110 (MQ=255) aGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaactttggttaaaaaataaaatgga < 2:16773‑M2/141‑38 (MQ=255) aggaggTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTATTCGAACTTACGTTCCGCTAGAGAAGAACGTTGCCAGGCAgttttttaatcaaattttggttcaaaaataaaatggtaaag < 2:21139‑M2/141‑42 (MQ=255) acCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGCCCGCGAGGACCCGCATTGAGTCCGTAAGGTCTCATATTatatc > 2:62840/1‑140 (MQ=11) | CTGACGAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTA‑CATTCATATG‑TCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATG > USA300TCH1516_ALE/517593‑517865 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |