Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,497	0	A	C	45.0%	58.5 / 10.9	41	V288V (GTA→GTC)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base A (17/5);  new base C (0/18);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 3.35e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTTCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAG  >  NC_000913/436353‑436641                                                                                                                                                 |                                                                                                                                                   gTTTTCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGttt                                                                                                                                             >  2:216941/1‑151 (MQ=255)   tttCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTAc                                                                                                                                           >  2:166771/1‑151 (MQ=255)   tttCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTAc                                                                                                                                           >  1:629843/1‑151 (MQ=255)        gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCt                                                                                                                                         <  1:780007/148‑1 (MQ=255)        gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCt                                                                                                                                         <  1:695174/148‑1 (MQ=255)          tGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATc                                                                                                                                   >  1:252361/1‑151 (MQ=255)            cgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCgg                                                                                                                                 >  1:478601/1‑151 (MQ=255)                      ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGAcc                                                                                                                       >  1:734946/1‑151 (MQ=255)                                         gcgctgcgcgGGGCGCTCTCTGGCGGTGAAGATTACGGGTTGTTTTTCACTGTGCCGGAACTGAACCGGGGCGCGCGGGATGTGGCTCTCGGACACCGGGGCGTAC‑CGTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCttt                                                                                                    <  2:373885/151‑1 (MQ=255)                                                   gggCGCTCTCTGGCGGTAAAGATTCCGAGTTTTTTTTCCCTGTGCCGGAACTGACCCGGGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTCCTTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                            <  1:930623/149‑1 (MQ=255)                                                   gggCGCTCTCGGGCGGGGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGGTGGTTGTGGCTCTCGGACCCCTGGGCGTCC‑CGTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                           <  2:633335/150‑1 (MQ=255)                                                    gggcttttgaggCGGTGAAGTTCAGGGGTTGTTTTTCTCTGTGCCGGAACAGAGCCTGGGCGCGCTGGGTGTGGTTCTCGG‑TACC‑GGGGGTCCACCTTTACCCGATCTCGGTCAAAGGACCGCCGATATCGAAGGGCTTTGTTTTATTc                                                                                           <  2:245164/139‑1 (MQ=255)                                                    ggCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                         >  1:867857/1‑151 (MQ=255)                                                              ggCGGTGAAGATTCCGTGTGTTGTTTCCCTGGGCCGGAACTGACCCGTGGCGCGTTGGATGGGGCTCTCGAACACGTGGGCTTCC‑CTTTTCCTTG‑TTTCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGc                                                                                   <  1:148217/147‑1 (MQ=255)                                                                cGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                             >  1:51071/1‑151 (MQ=255)                                                                         ttAGGAGTTGTGTTTCTCTGTGCCGGAACTGACCCGGGGCGCGCGGGTTGTGGCTCTCGGACCCCGGGGCGTCC‑CGTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                     <  2:502318/150‑1 (MQ=255)                                                                          tACGAGTTGTTTTTCACTGTGCCGAAACTGAACCGTGGCGCGTTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTa                                                                    <  2:221150/150‑1 (MQ=255)                                                                              aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                               >  1:896529/1‑151 (MQ=255)                                                                               gttgttTTCCTCTGTGCCGGAACGGACCCGGGGCGCGGTGGAGGTGGTTGGGGGACCCGGGGGTGTCC‑CGTTTCCCTG‑TCCGGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                <  2:590375/149‑1 (MQ=255)                                                                                   tgtTTCCCTGTGCCGGAACTGACCCGTGGCGCGCTGGATGTGGCTCGCGGACCCCTGGGCGTCC‑CTTTTCCCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaaa                                                           <  1:268026/150‑1 (MQ=255)                                                                                    gtTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAgg                                                         >  1:542789/1‑151 (MQ=255)                                                                                        cgcTGTGCGGGAACTGACCGGTGGCGCGCTGGATGTGGCTCTCGGACCCCTGGGCGTCC‑CTTTTACCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTGCATTAGACTGGAAAGGatat                                                     <  2:585769/149‑1 (MQ=255)                                                                                               ccGGACTTGACCCGTGGCGCGCTGGATGTGGCTCTCGGCCACCTGGGCGTCC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                      <  2:162625/143‑1 (MQ=255)                                                                                                cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                             >  1:134908/1‑151 (MQ=255)                                                                                                cGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAttt                                             >  2:701696/1‑151 (MQ=255)                                                                                                 ggACCTGACCGGGGGCGCGTTGGATGTGGCTCTCGGACACCGGGGCGTCC‑CTTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATg                                                    <  2:312024/143‑1 (MQ=255)                                                                                                 ggAACTGAACCGTGGCGCGTGGGATGGGGCTCTCGGACCCCGGGGCGTCC‑CGTTTCCCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtt                                              <  2:354897/149‑1 (MQ=255)                                                                                                  gAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                           >  2:407965/1‑151 (MQ=255)                                                                                                   aaCTGAACCGGGGCGCGGTGGATGTGGCTCGCGGACCCCTGGGCGTAC‑CGTTTACCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                            <  1:925911/149‑1 (MQ=255)                                                                                                     cggAACGGTGGCGCGTGGGGTGGGGCTCGGGGACGCGTGGGTGTGC‑GTTTTACCTG‑TAGCGGGAAAATGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                        <  2:148442/149‑1 (MQ=255)                                                                                                             tGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                 >  2:507854/1‑150 (MQ=255)                                                                                                              ggggcggtggtggtgGCTCTGGCCCCCCGGGGCGTCC‑CTTTTCCTTT‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaaa                               <  1:238175/139‑1 (MQ=255)                                                                                                                     tGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcg                        >  1:68633/1‑151 (MQ=255)                                                                                                                       gATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                      >  2:316322/1‑151 (MQ=255)                                                                                                                            ggCTCTCGGACACTGGGGCGTCC‑CGTTTCCCTT‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                 <  2:929967/151‑1 (MQ=255)                                                                                                                              ctctCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc               >  2:881367/1‑151 (MQ=255)                                                                                                                               tctgGGACCCGTGGGCGACC‑GGTTTCCCTG‑TGTGGGGAAATGGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTc               <  1:238349/150‑1 (MQ=255)                                                                                                                                   ggccccgggggCGTCC‑TTTTTCCTTG‑TAGCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAg                 <  1:689208/136‑1 (MQ=255)                                                                                                                                   ggACCCCGGGGCTTCC‑CTTTTCCCTG‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGcc            <  1:438262/149‑1 (MQ=255)                                                                                                                                          ggggCTTAC‑TGTTTCCCTT‑TATGGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGa   <  1:85990/150‑1 (MQ=255)                                                                                                                                           gggCGTCC‑CTTTTCCCTG‑TATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAg  <  1:736904/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GTTTTCTGATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTAC‑CGTTTACCTG‑TATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAG  >  NC_000913/436353‑436641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑