| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,812 | 0 | G | A | 69.4% | 60.3 / 34.7 | 50 | intergenic (‑895/‑273) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (6/9); new base A (18/16); total (24/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.38e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAA > CP000730/1929666‑1929957 | ataaAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagta > 1:582641/1‑149 (MQ=255) tttCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTAtctc > 1:233372/1‑149 (MQ=255) tttCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCGAtctc > 1:17996/1‑149 (MQ=255) aaTTTGTCCAATTAAGTGTAGACCATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGgt < 1:72467/149‑1 (MQ=255) gtgtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCt > 1:35893/1‑149 (MQ=255) tCAATCTACAAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTc < 1:154539/149‑1 (MQ=255) cAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGc < 1:36720/149‑1 (MQ=255) cAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGc < 1:415637/149‑1 (MQ=255) aaacAAGTCACTGTGCTTGTATATTTGCCTCTGATATAATACTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAAAGGAGGTG‑TA‑TAA‑G‑G‑GGATGCTTATTTTCGTTCACATCATAGCACCAGTAATCAGTGGCTGTGCCAt < 1:235881/146‑1 (MQ=255) aagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTTTTGCGt > 1:7118/10‑149 (MQ=255) aagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt < 1:38485/140‑1 (MQ=255) agtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGta < 1:565592/141‑2 (MQ=255) agtagatatgCTTGTATATTCACAGATGGTATAATAATAGACTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGta < 1:23765/141‑2 (MQ=255) tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 1:215227/143‑1 (MQ=255) tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 1:474952/143‑1 (MQ=255) ctatgCTTGCATATTCCCAGCTGGTATAATAATAGAGTCGCCTATCCCTCCG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTA‑C‑TTTGCTAATCATTTTCGTTCACATCATAGCACCCGTCATCAGTGGCTGTGCTGTTGCGtattata < 1:185145/146‑7 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatact < 1:48470/148‑9 (MQ=255) gCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTa > 1:512408/1‑149 (MQ=255) gCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCGGTGGCTGTGCTGTTGCGTATTATACttt > 1:167219/1‑148 (MQ=255) ttGTATCTTTCCCGATGATATAATAGTAGAGTCGCCTCACTCTAAGCACATC‑GTGAACACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAt < 1:166137/149‑1 (MQ=255) ttGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCCCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAt < 1:369984/149‑1 (MQ=255) tgtatattcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTA‑CTT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 1:518630/13‑149 (MQ=255) tGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCAGAGAAGCAGGCATCAGTGGCTGTGCTGTTGCGtatgatactgattg > 1:462657/1‑136 (MQ=255) gTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTgg < 1:257741/149‑1 (MQ=255) tatattcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTA‑C‑TTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc < 1:230245/139‑1 (MQ=255) tataTTCACAGATGGTATAATAATAGTGTCGCCTATCTATCAG‑GCGGCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc < 1:261608/149‑1 (MQ=255) tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCCAAT‑‑CACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt < 1:194333/141‑2 (MQ=255) tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt < 1:601968/141‑2 (MQ=255) tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt < 1:370698/141‑2 (MQ=255) attcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGGGGAGATGCGT‑TAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGGGTATTATACTTATTTGCtta > 1:499020/8‑147 (MQ=255) ttGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAg < 1:225705/149‑1 (MQ=255) ttGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAg < 1:343109/149‑1 (MQ=255) tcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAATAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt > 1:262933/6‑149 (MQ=255) tcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCGCCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt > 1:441762/6‑149 (MQ=255) tcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑G‑T‑TGCTAATCATTTTCGTTCGCATCATAGCACCAGTCATCAGTGGCTGGGCTGTTGCGTATTATACTTGTTGGCTTAGt > 1:43040/6‑149 (MQ=255) tcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGATGTTACGTATTATACTTATTGGCTTAGt > 1:337920/6‑149 (MQ=255) tcacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAAGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTGCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTCGcgtagt > 1:15390/6‑144 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTTGCTTAGTa > 1:149264/5‑149 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa > 1:35678/5‑149 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa > 1:53496/5‑149 (MQ=255) cagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa > 1:345128/3‑147 (MQ=255) cagatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa > 1:552474/3‑147 (MQ=255) agatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaac > 1:383103/2‑146 (MQ=255) agatggtATAATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAAc > 1:134331/2‑149 (MQ=255) gatgatATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGGTTTTTTCTTATTGGCTAAGTAGAc > 1:139920/1‑149 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGATGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:547621/146‑1 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:485990/146‑1 (MQ=255) ggggataataataGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CA‑TTA‑C‑TTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa < 1:458035/145‑1 (MQ=255) ggtataATAATAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaa < 1:261591/147‑1 (MQ=255) gatATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCa < 1:375986/149‑1 (MQ=255) atatAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCaa > 1:83399/1‑149 (MQ=255) ataataataGAGTCGCCTATCTCTCAG‑GCGTCAAGT‑‑GACGAAGAGAGGAGGTG‑CATTAC‑T‑A‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa < 1:138827/149‑4 (MQ=255) ataataGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATa > 1:487375/1‑149 (MQ=255) aataatAGAGTCGCCTATCTCTCAG‑GCGTCAATT‑‑GGCGAAGAGAGGAGGTG‑CATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATCGCACCCGTCATCAGTGGCTGTGCTGTTGCGTGTTAGACTTATTGGGTTAGTacgccccgcaagt > 1:153926/1‑137 (MQ=255) | ATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAG‑GCGTCAATTTAGACGCAGAGAGGAGGTG‑TA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAA > CP000730/1929666‑1929957 |
| 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: ‑ |