| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,918 | 0 | A | G | 55.3% | 13.2 / 54.8 | 47 | intergenic (‑1001/‑167) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (15/6); new base G (13/13); total (28/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.32e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTT > CP000730/1929779‑1930047 | gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt < 2:273126/141‑1 (MQ=255) aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt > 1:112630/1‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:30257/2‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:33327/2‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:375929/2‑141 (MQ=255) atgCTTGAATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:346363/2‑141 (MQ=255) cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 1:84924/141‑4 (MQ=255) cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 2:282629/141‑4 (MQ=255) tgtatattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat > 1:355259/13‑139 (MQ=255) tGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat < 2:54947/141‑6 (MQ=255) gTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattata < 2:306512/141‑4 (MQ=255) tataTTCACAGATGGTATAATAAGATAGGCGCCTAGCTCTCAGTCTTCAAGTT‑‑ACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatac < 1:35682/141‑8 (MQ=255) atatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTc < 1:221634/141‑1 (MQ=255) tatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCt > 1:89552/1‑141 (MQ=255) tatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCt < 1:210547/141‑1 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 1:363942/5‑141 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGACGAGGTGCA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 2:386019/5‑141 (MQ=255) ccGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCG‑TTTTTTCTTATTGGc > 1:28364/1‑141 (MQ=255) agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt < 2:4715/140‑1 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag < 1:13671/138‑4 (MQ=255) tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa > 1:336769/1‑141 (MQ=255) ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt < 2:374386/139‑1 (MQ=255) gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa > 1:294388/2‑141 (MQ=255) ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa > 2:185738/1‑139 (MQ=255) ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 1:145567/137‑1 (MQ=255) ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTACTCATTTTCGTTAATATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 1:175012/141‑1 (MQ=255) ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:91601/141‑1 (MQ=255) agtagAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt < 2:295419/109‑1 (MQ=255) agtagAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt > 1:295419/1‑109 (MQ=255) aatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaa < 1:94330/139‑1 (MQ=255) tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca > 1:183396/1‑139 (MQ=255) agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa < 1:1140/141‑4 (MQ=255) agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa > 1:158384/1‑138 (MQ=255) gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGATTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGTCATTGCGTTTTTTTCTTATTGTCTAAGTGGACGCAATAcga > 2:255374/1‑139 (MQ=255) ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta > 2:331641/1‑131 (MQ=255) cTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAg > 1:329472/1‑141 (MQ=255) gACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATa > 1:380442/1‑141 (MQ=255) gaggagGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATccc > 2:340035/1‑141 (MQ=255) cGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTTTTTTTTGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGTTTAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCCCAAATAGTGAGTGGATTgt > 2:261234/1‑140 (MQ=255) tcatAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCAACAAATAATTAATAGGCGACTTTATAAGCCAGCATCGA‑AAAAATCCCCACACTACTGC‑AATAGTGTGGGGATTGgtgc > 1:216278/1‑140 (MQ=255) gCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAAt < 2:112630/141‑1 (MQ=255) ccAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGCC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGGGAGGGGAGTGGTGTATCAGTAAATACt > 1:349665/1‑141 (MQ=255) gTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTAt > 1:205122/1‑141 (MQ=255) tcatcaGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTAtt > 1:236309/1‑141 (MQ=255) tcatcaGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGAGATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCATATAGTGAGGGGATTGGTGTATAAGTAAATACTCAtt < 2:336769/141‑1 (MQ=255) gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt > 1:192713/1‑141 (MQ=255) gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt > 1:393358/1‑141 (MQ=255) | GACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATAC‑‑AA‑‑AATAGGTGAC‑ATAT‑AGCC‑GCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTT > CP000730/1929779‑1930047 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |