Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	45.1%	62.7 / 26.8	51	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (26/2);  new base A (0/23);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.52e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTT  >  NC_000913/436367‑436660                                                                                                                                                       |                                                                                                                                                   tttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGc                                                                                                                                                    >  2:270937/1‑150 (MQ=255)  ttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGc                                                                                                                                                    <  1:1005108/149‑1 (MQ=255)  ttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGc                                                                                                                                                    <  2:954698/149‑1 (MQ=255)  ttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑a                                                                                                                                                  >  2:614741/1‑150 (MQ=255)     tcGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATg                                                                                                                                              >  1:269557/1‑151 (MQ=255)         cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑ccg                                                                                                                                         >  1:281967/1‑151 (MQ=255)                      aaCAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGTAgg                                                                                                                            >  1:332520/1‑151 (MQ=255)                          ggCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCtt                                                                                                                        >  1:300373/1‑151 (MQ=255)                          ggCGCGGCGGGGGGCGCTTTGTGGGGGTGAAGATTACGAGTTGTTTTTCTCGGTGCCGGAA‑CTGAGCCGTGGCGCGTTGGTTGGGGCTCGCGGACACGGGGGCGTCCCGTTTCCCTGTATGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCtt                                                                                                                        <  1:707293/151‑1 (MQ=255)                           gcgctgcgcgGGGCCCTCTGTGGCGGTAAAGATTACGTTTTGTTTTTCCCTGGGCGGAAA‑CGGACCGGGGGCGCGCTGGTTGGGGCTCCCGGCCCCTGGGGCGTCCTTTTTCCTTGTAGCGGGA‑AAATGA‑CCGCCGATATCGAAGGGc                                                                                                                          <  2:611588/148‑1 (MQ=255)                                gcgcggGGCGCTCTCGGGGGGTGAATATTAGGATTTGTTTTTCACTGTGCGGAAA‑CTGACCGGGGGCGGGTTGGTTGTGCCTCCCGGACACGGGGGCGTCCTTTTTCCCTGTAGCGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTg                                                                                                                      <  2:69240/147‑1 (MQ=255)                                 cggggggCGCTCTCGGGCGGGGAAGATTCCGGGTGGTTTTTCCCTGTCCCGGAA‑CTAACCCGGGGGGGGCGGGTTGTGCCTCCCGGCCCCGTGGGCGTCCCTTTTCCTGGTCTGGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGtttt                                                                                                                  <  2:317039/146‑1 (MQ=255)                                     gggCGCTCTGGGGGGGTGAAGTTTACG‑GTTTTTTTTTCCCGGGCCGGAACCTAACCCGGGGGGCGTGGGTTGTGGCCCCCGCCCCCTTGGGCGTCCTTTTTACTTTTAGGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTAtt                                                                                                               <  2:658875/149‑1 (MQ=255)                                     gggCGCTCTCGGGGGGTGAAGATTACGGGTTTTTTTTCCCTGTGCCGAAA‑CTAACCGGGGGCGCGGTGGGTGTGGCTCCCGGACACCTGGGCGTCCTTTTTACTTGTATGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGtttt                                                                                                                  <  2:104450/146‑1 (MQ=255)                                      ggCGCTCTCGGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCGGAAA‑CTGACCGGGGGCGCGCTGGTTGTGGCTCTCGGACCCCGGGGCGTCCCTTTTCCTTGTATCGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGt                                                                                                            <  1:1012879/151‑1 (MQ=255)                                          ctctctGGGGGTGAAGTTTCGGTTTTTTTTTTCACTGTCCCGGAA‑CTGACCGGTGGCGCGGGGGATGTGGCTCTCGGACACTGGGGGGTCCTTTTTCCTTTTAGCGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGa                                                                                                          <  2:1084893/149‑1 (MQ=255)                                          ctctctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACg                                                                                                        >  1:287468/1‑151 (MQ=255)                                           tctctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACgg                                                                                                       >  2:866970/1‑151 (MQ=255)                                               tGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGa                                                                                                    >  1:999696/1‑150 (MQ=255)                                                  cGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCt                                                                                                >  2:452079/1‑151 (MQ=255)                                                   ggTAAAGATTACGGTTTGTTTTTCTCTGTGCCGAAA‑CTGACCCGGGGCGCGCTGGTTGTGGCTCTCGGACACCTGGGCGTCCCTTTTACCTGTATCGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAAcc                                                                                                 <  1:721607/149‑1 (MQ=255)                                                        aGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTAc                                                                                           >  2:405966/1‑150 (MQ=255)                                                          aTTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                        >  2:982276/1‑151 (MQ=255)                                                           ttACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACAtt                                                                                        >  2:68687/1‑150 (MQ=255)                                                             aCGTGTTGTTTTTCCCTGTGCCGAAA‑CTGAACCGTGGCGCGCTGGTTGTGCCTCTCGCCCCCCGGGGCGTCCCGTTTCCCTGTATGGGCA‑AAAGGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                                      <  1:106185/150‑1 (MQ=255)                                                                tgttgttTTCCACGGTGCCGAAA‑CTGAACCGTGCCGGGGTGGTTGTGCCTCTCGGACACCGGGGCTTTCTTTTTCCCTGT‑GCGGGCAAAATGC‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACt                                                                                   <  2:566156/149‑1 (MQ=255)                                                                  ttGTTTTTCTCTGTGCCGGAA‑CTGACCCGGGGCGCGCTGGATGTGGCTCTCGGCCACGGGGGCGTCCTGTTTCCCTGTAGGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                 <  1:715863/150‑1 (MQ=255)                                                                      gtTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCAGGATGTGGCTCTCGCACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAg                                                                             >  2:46411/1‑150 (MQ=255)                                                                       tttCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAgg                                                                            >  1:986461/1‑150 (MQ=255)                                                                        ttCCCTGTGCAGAAA‑ATGAACCGTGGCGGGGTGGAATGGCCCCTCAGACTCGGGGGAGCACCTTTAACTTGTATGGAGC‑AATTTA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTgg                                                                                 <  1:712349/144‑1 (MQ=255)                                                                                gCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                                  >  2:879119/1‑151 (MQ=255)                                                                                 ccGGAA‑CTGAACCGGGGCGCGCGGGATGTGCCTCCCGGACCCCTGGGCGTCCCTTTTCCCTGTAGGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtt                                                                 <  1:476153/151‑1 (MQ=255)                                                                                   ggAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                               >  1:1105101/1‑151 (MQ=255)                                                                                   gaaa‑CTGACCCGTGGGGCGTTGGTTGTGGCTCTCGGCCACGTGGGCTTCCCTTTTCCCTGTAGCGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                                  <  2:848421/146‑1 (MQ=255)                                                                                     aa‑CTGACCCGTGGCGCGCTGGTTGTGGCTCTCGGACACCGGGGCGTACCTTTTCCCTGTATCGGTA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                                              <  1:731860/150‑1 (MQ=255)                                                                                           acccGTGGCGCGTGGGATGGGTCTCCCGGACCCGGGGGCTTCCCTTTTCCTTGTGTGGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                           <  2:609324/146‑1 (MQ=255)                                                                                                 ggCGCGCGGGAGGGGGCTCGCGGCCCCGGGGGCGTCCCTTTTCCCTGTATCGGGA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCa                                                           <  2:830026/142‑1 (MQ=255)                                                                                                    gcgcTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                                   >  2:355725/1‑147 (MQ=255)                                                                                                     cgcTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATg                                              >  2:640360/1‑151 (MQ=255)                                                                                                      gcTGGACGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGt                                             >  2:15902/1‑151 (MQ=255)                                                                                                             ggggCTCTCGGCCCCGGGGGCGTCCCTTTTCCTTTTACGGGGA‑AAAGGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGaa                                       <  1:1050328/148‑1 (MQ=255)                                                                                                                  tctcGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                                 >  2:1009010/1‑151 (MQ=255)                                                                                                                    cccgcccccgggggGTTCCGTTTTCCTTTTACGGGA‑AAAAGGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACAGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAg                                                 <  2:1066416/124‑1 (MQ=255)                                                                                                                      ggACACGGGGGCGTCCCTTTTCCTTGTAGCGGGA‑AAATGC‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCg                                 <  2:760503/147‑1 (MQ=255)                                                                                                                         ccccTGGGCGTACTTTTTCCCTTTAGGGGAA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGaa                           <  1:287846/148‑1 (MQ=255)                                                                                                                          acCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGa                            >  1:31462/1‑148 (MQ=255)                                                                                                                                 cGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTa                   >  2:394659/1‑150 (MQ=255)                                                                                                                                  gTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAAt                 >  2:192231/1‑151 (MQ=255)                                                                                                                                   tacgttttCCCTGTAGCGGCA‑AAATAA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTaa                  <  2:401635/144‑1 (MQ=255)                                                                                                                                     ctttttccttGTATCGGGA‑AAAGGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTa                   <  1:84096/137‑1 (MQ=255)                                                                                                                                         ttACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGc          >  2:1105860/1‑151 (MQ=255)                                                                                                                                         ttACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGc          >  1:1034175/1‑151 (MQ=255)                                                                                                                                                 aTCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACtt  >  2:679048/1‑151 (MQ=255)                                                                                                                                                    gggA‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACt   <  1:340826/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   TTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAA‑CTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAATGA‑CCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCGTGGCATCTACTT  >  NC_000913/436367‑436660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑