| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 517,732 | T→C | 39.7% | intergenic (+5800/‑963) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 517,732 | 0 | T | C | 39.7% | ‑3.5 / 24.1 | 31 | intergenic (+5800/‑963) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| Reads supporting (aligned to +/- strand): ref base T (10/9); new base C (2/10); total (12/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.52e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.50e-01 | |||||||||||
ACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGT > USA300TCH1516_ALE/517602‑517866 | aCTAATCGATCTAAGACTTAATCAAAATAAATATTTTGCAAAACAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATTTCTGTTGAATATAACAAGGAGGTCAAACCTGTTTCAAtt > 1:101264/1‑135 (MQ=11) tAAGCGATCGAAGAGTTAATCAAAAGAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTAGAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGcc < 2:14148/136‑1 (MQ=255) aaTCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTACATAcca > 2:145701/1‑135 (MQ=9) gatctaAGACTTAATCAAAATATAGGTGTTGAGAAGTAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑Aaca < 2:41070/136‑1 (MQ=11) gatcgaAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTTTGGTGACTATAGTAATTAGGTTATACCTGTTTCAATGCCG‑Aaca < 1:113552/136‑1 (MQ=11) gatcgaAAACGTAATCAAAATAAATGTTTTGCTAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑Aaca < 2:150864/136‑1 (MQ=16) tAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCATTTCTTTTTTCATGCCG‑AACACAGAAGTTAAg < 1:81677/136‑1 (MQ=11) aaacAAAATAAATGTTTTGTGAATCAAACACACTTTTACCTACCACCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACTTGTTTCCATGTCG‑AACAAAGAAGGTAAGc < 1:13809/133‑1 (MQ=11) tGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCg < 1:76840/136‑1 (MQ=33) aaaTCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACt < 1:134821/136‑1 (MQ=33) aaTAACTTGTACATACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCAGTTTCCATGCCG‑AACACAGAAGTTACGATCCTTCGCGTCGATGTTAGTCGGACta > 2:31998/1‑135 (MQ=11) tttACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTGGAACTTAAGTTcc > 2:73368/1‑136 (MQ=17) gTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACATGTTTATA‑GCAGAAACACAGCCGCTTCACTCGCTATTGTCGATTGTAGTCGAACTTACGTTCCGCTGGTGGAGAAGCTTGCCAGGcg > 2:105059/1‑135 (MQ=2) aTTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCAAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCaaaaaaa > 2:71139/1‑135 (MQ=17) aTTCATATGTCTGGTGACTTTAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTTCGCTAGAGTAGAATTTTGTCAGGCAAAAAAGGGagg < 1:75113/136‑3 (MQ=11) ttCATATGTCTGGTAACAAAAAAAAAAAAAACACACCTATTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatca < 1:63044‑M2/136‑13 (MQ=255) atatGTCTGGTGCCTATAGCAAGGAGGTCACACCTGTTCACATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaat < 1:93302‑M2/136‑16 (MQ=255) atatGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTTGAATTTACGTTCTGTTAGAGTAGAATGTTGTTAGGCAgttttttaatcaaat > 1:50929‑M2/1‑121 (MQ=255) gTCTGGTGACTATAGCAAGGAGGTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACTTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttg < 2:57276‑M2/136‑20 (MQ=255) cTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAGCGTTGCCAGGCAAAAAATGGATGCGATGAGCCg > 1:114669/1‑136 (MQ=17) gACTATAGCAAGGAGGTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttctaatcaaattttggttaaca < 2:39917‑M2/136‑27 (MQ=255) tataGCAAGGAGGTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCACTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaaa < 2:49301‑M2/136‑30 (MQ=255) taGCAAGGAGGTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCATTAGCGTCGATGGTAGTAGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaacaa < 2:55266‑M2/136‑32 (MQ=255) aGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCg > 1:124047/1‑136 (MQ=32) gaggTCACACGTGTTCCCATGCCG‑AACACAGAAGATAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAAGGTTGCCAGGCAgttgtgtaatcacattttggtaaaaaaataaaatggac < 2:15083‑M2/136‑39 (MQ=255) gaggTCACACCTGTTTCCATGCCA‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGt > 1:155452/1‑136 (MQ=17) aggTCACACCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttattcaaattttggttaaaaaataaaatggaca > 1:155318‑M2/1‑97 (MQ=255) cacaCCTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataaaatggacaagat < 1:154229‑M2/136‑44 (MQ=255) ccTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCAGCATTGAGACCGCCAGATAACtttttt > 2:37695/1‑136 (MQ=11) ccTGTTCCCATGCCG‑AAAACAAAAGTTAAGCTACTTAGCGTCGAAGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataaaatggacaagataaaa < 1:136286‑M2/136‑48 (MQ=255) cTGTTCCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataaaatggacaagataaaaa < 2:17805‑M2/136‑49 (MQ=255) ttCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATTAGCCGCATTGATACCGCAAGGTCTCTTTTTTTATGt < 1:123325/136‑1 (MQ=18) | ACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCG‑AACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGT > USA300TCH1516_ALE/517602‑517866 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |