Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,829	0	G	A	46.8%	28.0 / 25.5	47	L47F (CTT→TTT)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (8/17);  new base A (22/0);  total (30/17)
Fisher's exact test for biased strand distribution p-value = 4.04e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCC  >  NC_000913/3947683‑3947977                                                                                                                                                     |                                                                                                                                                       ggCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAgggt                                                                                                                                                     >  2:595247/1‑148 (MQ=255)    aCCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTcaca                                                                                                                                                 <  1:246923/151‑1 (MQ=255)      cGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCacac                                                                                                                                                <  1:610353/150‑1 (MQ=255)        aTAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCa                                                                                                                                             <  1:348481/151‑1 (MQ=255)         tAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAGGGTCACAccc                                                                                                                                              >  2:462171/1‑149 (MQ=255)          aGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTTACCAcccgt                                                                                                                                            >  1:447585/1‑149 (MQ=255)          aGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGTG‑GGAAAgg                                                                                                                                                       >  1:254940/1‑139 (MQ=255)          aGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCACAccc                                                                                                                                              >  1:484301/1‑148 (MQ=255)           gAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGTTTACACCCACtt                                                                                                                                          >  1:103972/1‑151 (MQ=255)             aaaCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTCACACCCAggt                                                                                                                                          >  2:755589/1‑147 (MQ=255)               aCTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑tt                                                                                                                                     <  1:781979/151‑1 (MQ=255)                       tGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GGAAAGGTTCCCAACCAGGTGG‑ATTTTCAGtt                                                                                                                             >  1:596434/1‑151 (MQ=255)                       tGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCACACCCCGGTGC‑TTTTTCCGtt                                                                                                                             >  2:635981/1‑151 (MQ=255)                        gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGG‑GAAAAGGTT‑ATACCCCGTTGT‑TTTTTCAGtt                                                                                                                             >  1:501033/1‑150 (MQ=255)                        gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GGAAAAGGTCACACCCCGTTGA‑TTTTTCTGtt                                                                                                                             >  1:772623/1‑150 (MQ=255)                        gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCCCACCCCGTTGG‑TTTTTCTGttt                                                                                                                            >  1:677867/1‑150 (MQ=255)                                         aCCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GGAAAAGGTCACACCCCGTTGG‑TTTTTCCGTTTTTTGTTTCGaaa                                                                                                                >  2:328879/1‑146 (MQ=255)                                           ctcctTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGGTTACACCCCGGTGA‑TTTTTCCGTTGTTTTATTTGAAAACTCa                                                                                                           >  2:194495/1‑149 (MQ=255)                                               ttACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAGGGTCACACCCACATGATTTTTCCAGTT‑TTTGATTCCAAAGCTCCctgc                                                                                                       >  2:93813/1‑149 (MQ=255)                                                                 gTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCg                                                                                   <  1:175295/151‑1 (MQ=255)                                                                    cTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGGTCACACCCACTTGA‑TTTTTCTGTTTTTTTATTTGAAAACTCACTGCTGACTGGGGCAGaaaaaacgaat                                                                                >  1:749280/1‑141 (MQ=255)                                                                              tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTCACACCCAGGTGG‑TTTTTCCGTTGGCTGATTCGAAAGATCACTGCTGACTGGGGCCGATAGAGCGATTCAGCCGCTc                                                                       >  2:273168/1‑150 (MQ=255)                                                                                       aaGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGTTCACACCCAGTTGA‑TTTTTCAGTTGTCTTATTTGAAAGATCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCCCGA‑CCaaa                                                               >  2:713985/1‑148 (MQ=255)                                                                                         ggCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGAc                                                          <  1:139476/151‑1 (MQ=255)                                                                                           cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGTTCACACCCCGTTGA‑TTTTTCCGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCCGATAGAGGGATTTAGCCGCTCCA‑CCAAAggg                                                            >  2:303249/1‑145 (MQ=255)                                                                                             gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGTTCACACCCACTTGA‑TTTTTTAGTTTTTTGATTCGCAAAATCACTGCTGACTTGGGGCGATAGAGCGAGTTAGCCGCCCCA‑CCaaaacgaccc                                                        >  1:523626/1‑142 (MQ=255)                                                                                               agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGtt                                                     <  1:778972/150‑1 (MQ=255)                                                                                               agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTc                                                    <  1:378026/151‑1 (MQ=255)                                                                                                gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GTAAAAGGTCACACCCCCCTGA‑TTTTTCAGTTTTCTTGTTTGAAAGATCACTGCTGACGGGGGCCGATAAAGCGCTTCAGCCGCCCGA‑CCAAAAAGAcgcg                                                       >  1:183173/1‑147 (MQ=255)                                                                                                 tttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑TTAAAAGGGCTGACCCCGATTA‑TTTTTCTAGTGGCTGTTTCGAAAGATAACCGCTTACTGGGGGAGGTAAAGAGGTTGAAACGCCCGA‑ACAAAATGGcgcggtggg                                                  >  1:567503/1‑146 (MQ=255)                                                                                                 tttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTCACACCCAGTTGA‑TTTTTCAGTTGTTTTGTTCGAAAACTCACTTCTGACTGGGTCAGATAAAGCGATTCAGCCCCCCGA‑CCAAAAGGACGCGTTTgg                                                  >  2:668188/1‑151 (MQ=255)                                                                                                    ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCt                                                <  2:530489/150‑1 (MQ=255)                                                                                                     tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTa                                               <  2:174176/150‑1 (MQ=255)                                                                                                      cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GGAAAAGGTCGCACCCCCTTGT‑TTTTCCTGTTTTCTGGTTTGGAAGCTCACCGCTGACTGGGTCAGATAGAACGATTCAAGCCCTCGA‑CCCAAGGGAAGCGTTTgg                                                  >  1:756663/1‑146 (MQ=255)                                                                                                         cGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGTTCACACCCAGTTGA‑TTTTTCCGTTTTCTGATTTGAAAACTCCCTGCTGACTGGGTCCGATAGAGCGATTCAGCCCCTCGA‑CCAAAGGGACGCGTTCGGCTAACtt                                           >  2:416957/1‑150 (MQ=255)                                                                                                             aGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGGAAAAGGTT‑ACACCCCGATGA‑TTTTTCAGTTTTTTGATTCTAAAACTCACTGCTGACTGGGTGAGATAGAGCGATTTCGCCGCTCGA‑CCCCAATGAGGCGGTCGGGTAACTTCCAgg                                      >  1:546734/1‑151 (MQ=255)                                                                                                                ggTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGaaa                                   <  2:550950/151‑1 (MQ=255)                                                                                                                ggTTAAACGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGTTTACCCCCAGTTTG‑TTTTTCAGTTGTTTGGTTCGAAAACTCACTGCTGACTGGGGCCGATAGAGCGATTTAGCCGCTCGA‑CCCAAATGACGCGTTTGGCTGACTTCCAGGaa                                    >  2:233472/1‑150 (MQ=255)                                                                                                                   tAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTTACCCCCAGGTGA‑TTTTTCCGTTGTCTTTTTCGAAAGCTCACCGCTGACTGGGGTAGATAAAGCGGTTAAACCCCCCGA‑TCAAAGAGACGGGTTTGGCTAACTTCCCGGaa                                    >  2:322771/1‑147 (MQ=255)                                                                                                                    aaaCGGATATTGTTTCTGTGGC‑GGGG‑GAAAAAGGTCACACCCAGTTGG‑TTTTTCAGTTTTTTTATTTGAAAACTCACTGCTGACTGGGTCAGATAAAGCGATTCAGCCGCTCGA‑CCCAAGTGAAGCGTTCGGCTTACTTCCCGGAAAGgtt                               >  2:92501/1‑151 (MQ=255)                                                                                                                        ggATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACGCCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGATGACTGGGTCAGATAGAGCGATTCAGCCGCTAGC‑CCAAAGTGACGCGTTCGGCTAACTTCCAGAAAAGTTTTTaa                           <  1:731878/151‑1 (MQ=255)                                                                                                                        ggATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTaa                           <  2:284284/151‑1 (MQ=255)                                                                                                                        ggATATTGTTTCTGTGGC‑GGGT‑GAAAAAGGTCACACCCAGGTGA‑TTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGGCTGGGGCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGAGACGCGTTCGGCTAACTTCCAGGGAAGttttt                             >  2:665120/1‑149 (MQ=255)                                                                                                                          atatTGTTTCTGTGGC‑GGGT‑GAAAAGGGTGCCACCCCGGTGT‑TTTTTCCGTTTTTTGGTTGGGAAGCTCCATTCTGACTGGGGCAGATAGAGCGATTTAGCCGCCCGACCCAAAGGGA‑GCGGTTTGGTTACTTCCAGGAAAGttttt                             >  1:751571/1‑147 (MQ=255)                                                                                                                                  tCTGTGGC‑GGGT‑GAAAAGGTTCTCTCCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGGCTGGGTCAGATAGAGCGATACAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTATCTTCCAGGAAAGTTTTTAACAATTCCg                   <  1:675163/149‑1 (MQ=255)                                                                                                                                  tCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGt                  <  1:225798/150‑1 (MQ=255)                                                                                                                                     gtgGC‑GGGT‑GAAAAGGTTCACTCCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTAt                <  1:731241/149‑1 (MQ=255)                                                                                                                                           gggT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGt         <  1:25936/151‑1 (MQ=255)                                                                                                                                                   aaGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTcc  >  1:774455/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       GGCACCGATAGAAAACTCGTTATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGT‑GAAAAGGTTCACACCCAGTTGA‑TTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGA‑CCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCC  >  NC_000913/3947683‑3947977

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑