Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | USA300TCH1516_ALE | 517,732 | T→C | 17.1% | intergenic (+5800/‑963) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | USA300TCH1516_ALE | 517,732 | 0 | T | C | 17.1% | 47.6 / 4.6 | 32 | intergenic (+5800/‑963) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
Reads supporting (aligned to +/- strand): ref base T (18/8); new base C (3/3); total (21/11) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 3.90e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTAAAA > USA300TCH1516_ALE/517598‑517872 | gAATACTAATCGATCGAAAACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTAGTAACTATAGCAAGAAGGTCACACCCGTTTCCATGc > 2:30096/1‑141 (MQ=11) aTACTAATCGATCGAACACTTAATCAAAATAGATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCg < 1:291427/141‑1 (MQ=17) cTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAac < 1:238044/141‑1 (MQ=32) tagaAGATTTAATCAAAATAAATGTTTTGCGAAGCAATATCAATTTTACTTACTATCTAGTTTTGAAGGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGt < 2:36194/139‑1 (MQ=255) aGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGGCACACCTGTTTCCATGCCGAAAACAGAAGTTAAg > 1:249663/1‑141 (MQ=17) aGACTTAATCAAAATAAATGTTTTGCGAAGCAAAAGCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAAGTCACACCTGTTTCCATGACGAACACAGAAGGTAAg > 2:91148/1‑141 (MQ=255) aCTTAATCAATATTAATGTTTTGCGGAGCAAAAGCACTTTTACTTACTATCTAGTTTTGAATGGATAAATTACATTCATATGTCTGGTGACTATAGCAAGTAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCt < 2:44606/141‑1 (MQ=11) cTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTc > 2:257502/1‑141 (MQ=32) aataaatGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTc > 1:125092/1‑141 (MQ=32) atGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTCGCGTCGATgg > 2:185521/1‑141 (MQ=17) ttGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTGCTTAGCGTCGATGGTAGTc > 1:174212/1‑141 (MQ=17) gCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCTTAATACATAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTa > 1:211788/1‑141 (MQ=255) tCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGCAGTTAAGCTACTTAGCGCCGATGGTAGTCGAACTTACGTTcc > 1:117187/1‑141 (MQ=12) ttttACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTa < 1:222969/141‑1 (MQ=32) ttttGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGGGTAGAAGGTTGCCAg > 1:159378/1‑141 (MQ=17) ttttGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAg < 1:257502/141‑1 (MQ=32) gAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCaa > 1:166984/1‑141 (MQ=32) aaTTAGCTTCATATGTCTTGGTACTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaat > 2:222683‑M2/1‑131 (MQ=255) aTTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGGAACAAATGGAGGCGGTg > 2:244110/1‑141 (MQ=255) ggttagTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCAGAACACAGAAGTTAAGTTCCTTAGCGTCGAGGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCAt < 1:129996/136‑1 (MQ=255) tGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTga > 1:70227/1‑141 (MQ=32) gTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTgcga > 1:8052/1‑141 (MQ=17) aCTATAGCAAGGAGGTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTCCGTTCCGCTAGAGTCGAACGTTGCCAGGCAgtttcttaatcaaattttgggtaaaaaatcaa < 2:175715‑M2/141‑33 (MQ=255) cTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTACATGCCTTCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGc > 1:292881/1‑141 (MQ=11) aggaggTCACACATGTTCCAATGACGAAGACAGAAGTTAAGCTCCTTAGCGTCGAGGGTAGTCGAAATTACGATCCGCTAGAGTAGAACGTTGACAGGCAgttttataatcaaattttggttaaaaaataaaatggacaag > 2:264798‑M2/1‑100 (MQ=255) ggTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGAAGTCGAACTTACGTTCCGCTAGAGAAGAACGTTGCAAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCACAAGGTCTCtttt > 1:32899/1‑141 (MQ=255) gTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCCAGAGCAGCACGTTGCCAGGCAgtttcttaatcaaattttggttaaaaactaaactggccaagctagc < 2:262919‑M2/141‑47 (MQ=255) gTCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGCAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGGCACGTAgttttgtaagcaaactttgcttgaaaactaaaaaagacaagataaa < 2:267922‑M2/141‑47 (MQ=255) tCACACCTGTTCCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAgttttttaatcaaattttggttaaaaaataaaatggacaagataaaa > 1:255208‑M2/1‑94 (MQ=255) tCAAACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGAATGGGATGACACGCATTGAGAAAGAAAGATCTCattttt > 2:63403/1‑141 (MQ=11) acCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTCGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTCTg > 1:92001/1‑141 (MQ=17) ccTGGTTCCATGCCGAACACAGAAGTTAAGCGCCTGAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCTAGGTCTCTTTTTTTATGt < 2:211788/141‑1 (MQ=255) tCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTaaaa > 1:289236/1‑141 (MQ=33) | GAATACTAATCGATCGAAGACTTAATCAAAATAAATGTTTTGCGAAGCAAAATCACTTTTACTTACTATCTAGTTTTGAATGTATAAATTACATTCATATGTCTGGTGACTATAGCAAGGAGGTCACACCTGTTTCCATGCCGAACACAGAAGTTAAGCTCCTTAGCGTCGATGGTAGTCGAACTTACGTTCCGCTAGAGTAGAACGTTGCCAGGCAAAAAATGGATGCGATGAGCCGCATTGAGACCGCAAGGTCTCTTTTTTTATGTCTAAAA > USA300TCH1516_ALE/517598‑517872 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |