Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,743,657	0	A	C	45.8%	68.4 / 18.6	49	T309P (ACC→CCC)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
Reads supporting (aligned to +/- strand):  ref base A (23/3);  new base C (0/22);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 8.48e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGCCCGCCGCCATTGAAA  >  NC_000913/3743507‑3743800                                                                                                                                                            |                                                                                                                                                 aTTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTt‑a‑cta                                                                                                                                                  <  2:701164/151‑1 (MQ=255)  tttCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTt‑a‑ctac                                                                                                                                                 >  2:688216/1‑151 (MQ=255)         aaTTTTTATTGCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCct‑gctg                                                                                                                                         <  2:432153/151‑1 (MQ=255)             tttATTGCCATTGACGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGCGCTGACGAAAATCAGGCCA‑TTTGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCg                                                                                                                                     >  2:658299/1‑151 (MQ=255)                   gCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAAc                                                                                                                                <  1:905960/150‑1 (MQ=255)                     cATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAAccgc                                                                                                                             >  1:71571/1‑151 (MQ=255)                      aTTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAAccgcc                                                                                                                            <  2:41655/151‑1 (MQ=255)                      aTTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAAccgcc                                                                                                                            >  1:315445/1‑151 (MQ=255)                                      ttACCGACGCCCCCTCCCGTGATCCCAAGCTGAAACACATCATGGTTTCCT‑TTACCAGCGCCGAGCGTCCTGACAAAAACCAGCCCA‑TTCGCTTCCC‑CGGCCAAGAATTT‑C‑CTCCCCG‑GTTGGCCGAAAACCGCCGTAACGGCATCACt                                                                                                              <  1:657486/149‑1 (MQ=255)                                         tCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTtg                                                                                                          >  1:314626/1‑150 (MQ=255)                                             cGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGAc                                                                                                     >  1:636292/1‑151 (MQ=255)                                                cccccccCGGGATCCCAGGCTGAAACGCATCATGGATTTCG‑TACCTGGCGCCGGGGGTGCGGCAAAAACCCAGCCCA‑TCCGCTTCCC‑CGGCAATGATTTT‑C‑CTCCCCG‑GGGGCCAAAAAACCGCCGTAACGGCATCACTGTTGATGACAGc                                                                                                  <  2:144329/150‑1 (MQ=255)                                                 ccccccCGGGATCCCAAGCTGAACCGCATCAGGGATTACG‑TTACTAGGGCGGGGGGTGCTGACAAAAACCAGGCCT‑TCCGCTTCCC‑CGCCCATAATTTT‑A‑CTCCCCG‑GCGGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCg                                                                                                 <  1:297931/151‑1 (MQ=255)                                                 ccccccCGCGATGCAAGGCTCCAACGCATAAGGGATTATT‑TTACTAGTGCCGAGCGTGATGACAAAAACCAGGCCT‑TCCTCTTCCC‑GGGCTAT‑AATTT‑ACCTCCCCT‑GCGGGCAAAAACCCGCCGTAACGGCATCACTGTTGATGACAg                                                                                                   <  2:352997/149‑1 (MQ=255)                                                     cccGGGATG‑CAACCTGCAACGCCTCATTGTATACGTTTCCTGGCCCCGGGGGTGCT‑ACCAAAAACCCGCCAGTCCGCTTCCC‑CGTCTTTAATTTT‑C‑CTCCCCG‑GCTGGCAAAAACCCGCCGTAACGGCATCACTGTTGATGACAGCGtgtg                                                                                             <  2:276511/151‑1 (MQ=255)                                                         cgATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGcc                                                                                         >  1:753689/1‑151 (MQ=255)                                                          gaggCCAAGCTGCAACGTATCGTGGTTTCCT‑TTACTAGTGCCGAGGGTGCTAAAAAAAATCAGGCCA‑TTCCTTTCCC‑CGCCCATGAATTT‑A‑CTCCCCT‑GCTGCCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTggg                                                                                           <  1:508551/145‑1 (MQ=255)                                                                aaGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATcc                                                                                  >  1:813523/1‑151 (MQ=255)                                                                aaGCGGCACCGCATCAGGGTTTTTT‑TTACTGGGGCCGAGCGTGCTGACAAAAATCGGCCCT‑TTCGTTTCCC‑GGGCAATAATTTT‑A‑CCCCCCG‑GCGGCCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCaa                                                                                       <  1:368887/146‑1 (MQ=255)                                                                    tgcacccaattatGGATTACT‑TTCCTGGTCCCGGGGGTGCTGACAAAAACCAGCCCT‑TTCCCTTCCC‑CGGCCATGATTTT‑C‑CTCCCCT‑GCGGGCAAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCa                                                                                 <  1:621116/137‑1 (MQ=255)                                                                     gCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCg                                                                             >  2:847520/1‑151 (MQ=255)                                                                       accgcgTCATGTATTACT‑TCACGAGTGGCGGGGGTGCTGAAGAAATGCAGGCTA‑‑TCCCTTACCGCGGCCATG‑ATTT‑G‑CCGCCCTGGCTGGCGAAAAGCCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGtt                                                                           <  2:45077/149‑1 (MQ=255)                                                                        aCGCATCATGGATTCCT‑TTACTAGTGCCGGGCGTGCTGACAAAAACCAGGCCT‑TTCCCTTCCC‑CGGCCATGATTTT‑A‑CTCCCCT‑GCGGCCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTa                                                                          <  1:34493/151‑1 (MQ=255)                                                                        aCGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGtt                                                                           >  2:737409/1‑150 (MQ=255)                                                                            atcatGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATg                                                                        >  1:575681/1‑149 (MQ=255)                                                                             tcatGGATTCCT‑TTCCTAGTGCCGAGCGTGCTGACAAAAACCAGGCCA‑TTCGCTCCCC‑CGGCCATGAATTT‑A‑CTCCCCT‑GCTGGCCAAAACCCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATga                                                                       <  1:349081/149‑1 (MQ=255)                                                                                 ggATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATgag                                                                      >  1:687475/1‑146 (MQ=255)                                                                                  gATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGAt                                                                 >  1:275774/1‑150 (MQ=255)                                                                                  gATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGAt                                                                 >  2:306607/1‑150 (MQ=255)                                                                                          ttctcgtcgCCGAGCGTCCCAACGAAATGCAGCCCT‑TCCTTTCACC‑CGCCCATAAATTT‑C‑CTCCCCG‑GAAGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTc                                                            <  1:808735/140‑1 (MQ=255)                                                                                             cTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGAtt                                                      >  2:977611/1‑151 (MQ=255)                                                                                                   cggggCGTGCGGAAAAAAACCGGGCCT‑TCCGCTCCCC‑CGCCCATGATTTT‑A‑CTCCCCG‑GCGGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGAtt                                                      <  1:754538/141‑1 (MQ=255)                                                                                                     gAGCGTGCTGACGAAAACCAGGCCA‑TTCGCTCCCC‑CGGCCATAATTTT‑A‑CCCCCCG‑GCGGGCAAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGa                                                <  1:176647/149‑1 (MQ=255)                                                                                                     gAGCGGGCTGCCAAAACGCGGGCCA‑TCCTCCTCCC‑CGCCAAAGATTTT‑G‑CTCCCCG‑GCTCGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATg                                                         <  2:412334/140‑1 (MQ=255)                                                                                                       gCGTGCTAACAAAAACCAGCCCT‑TTCGCTTCCC‑CGCCAATAATTTT‑A‑CCCCCCG‑GCGGCCAAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACata                                            <  2:286471/151‑1 (MQ=255)                                                                                                         gtgcaaaaaaaaaCCGGGCCA‑TCCCCTTCCC‑CGCCCAAAATTTT‑C‑CTCCCCT‑GCGGGACAAAACCCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGAttt                                                     <  2:880966/131‑1 (MQ=255)                                                                                                           gCTGACAAAAATCAGGCCT‑TCCCTTTCCC‑CGGCAATGAATTT‑A‑CTCCCCT‑GTTGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATcg                                         <  1:847146/150‑1 (MQ=255)                                                                                                                cGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGc                                   >  1:782951/1‑151 (MQ=255)                                                                                                                  aaaaGCAGGCAA‑TTCG‑TTCCC‑CCGCCAATAATTTCA‑CTCCCTT‑GCTGCCGAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACata                                            <  2:434808/140‑1 (MQ=255)                                                                                                                  aaaaACAGCCCA‑TCCCCTTCCC‑CGGAATTTATTTT‑C‑CTCCCCT‑CCGGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCa                                     <  2:882248/147‑1 (MQ=255)                                                                                                                   aaaCCAGCCCA‑TCCGCTTCCC‑CGGCAATAATTTT‑C‑CCCCCCT‑GCTGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCa                                <  2:416539/151‑1 (MQ=255)                                                                                                                       cAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATcc                            >  2:718684/1‑151 (MQ=255)                                                                                                                                tCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGtt                    >  2:1040587/1‑151 (MQ=255)                                                                                                                                 ctctcccc‑cGCCCATGATTTT‑A‑CTCCCCT‑GGGGGCCAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGtt                    <  1:12786/144‑1 (MQ=255)                                                                                                                                  gCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTg                  >  1:1019003/1‑151 (MQ=255)                                                                                                                                   ctcccc‑cGGCCTTAAATTT‑A‑CCCCCGT‑GGTGGCAAAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGcc                       <  2:739363/141‑1 (MQ=255)                                                                                                                                   cTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGc                 >  2:1071039/1‑151 (MQ=255)                                                                                                                                   cTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAAAGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGAAGCCCAATCTGTGCCGTTTg                  >  2:143275/1‑150 (MQ=255)                                                                                                                                      aCC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGcc                >  2:562704/1‑149 (MQ=255)                                                                                                                                          cggcccgggttttga‑ctccCCT‑GCGGCCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGCccgcc            <  2:743371/137‑1 (MQ=255)                                                                                                                                                    ttt‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGTCCGCCGCCATTGaaa  >  1:806183/1‑150 (MQ=255)                                                                                                                                                     tt‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGCCCGCCGCCATTGaaa  >  1:364143/1‑149 (MQ=255)                                                                                                                                                            |                                                                                                                                                 ATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGACGGTCCCACCCGCGATGCCAAGCTGCAACGCATCATGGATTACG‑TTACTAGTGCCGAGCGTGCTGACGAAAATCAGGCCA‑TTCGCTTACC‑CGGCCATGAATTT‑A‑CTACCCT‑GCTGGCCGAAAACCGCCGTAACGGCATCACTGTTGATGACAGCGTGTGGGCCAAAATCCAGGCGTTATGAGGAGATAAGTCATGATTTTTGGACATATCGCGCAGCCCAATCCGTGCCGTTTGCCCGCCGCCATTGAAA  >  NC_000913/3743507‑3743800

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑