Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	44.0%	67.5 / 20.3	50	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/5);  new base C (0/22);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 9.87e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATT  >  NC_000913/1376364‑1376651                                                                                                                                                  |                                                                                                                                                   ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                           <  2:144555/151‑1 (MQ=255)           cgccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAT‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                                  <  2:544796/150‑1 (MQ=255)                      cTGGACGGCGACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                                      >  1:287671/1‑151 (MQ=255)                        gggcGGCGCCCGAAAAATGGTGAGTGTTCCCCT‑GCGCGTACGGGAACGGGTCGCCGCGCGTCCCGGAA‑CGGTGGTTTATCTCGACCCGTTAAC‑CCGC‑TAGAAGGATCATATAATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                                    <  1:732661/148‑1 (MQ=255)                               gACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                             >  1:1016425/1‑151 (MQ=255)                               gACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                             >  1:866976/1‑151 (MQ=255)                               gACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                             >  1:117133/1‑151 (MQ=255)                                 ccGAAAAAGGGTGAGTGTTCCCCT‑GCGCGTAGGGGAAGAGGTCGCCGCGCGCACGGGAA‑CGGGGGTTTATCTCGACCCGTAAAC‑CCGC‑TATAAGTATCATATAACCACCCCCCCCCCAAAGGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                           <  1:929453/151‑1 (MQ=255)                                    aaaatTGGTGAGTG‑TTCCCTGGCGCGTACGGGACCAGGTCGCCGCGCGTCCCGGAC‑CGGTGGTTTATCGCGAACCTTAAAA‑CCGC‑TATCGGATTAATATGATCAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCt                                                                                                            <  2:491812/146‑1 (MQ=255)                                    aaaaaGGGTGGGTGTTCCCCG‑GCGGGTCCGGAAACGGGCCGCCGCGCGCCCCGAAC‑CGGTGGTGTACCCCG‑ACCCTTAAA‑CCCCTTTTAAGGATAATATAACCACCACCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                               <  1:761356/143‑1 (MQ=255)                                     aaaaTGGTGAGTGATCCCCT‑GCGGGTACGGAAACAGGTCGCCGCGCGTACCGAAC‑CGGTGGTGTATCTCAACCCTTTAAC‑CCGC‑TATAGGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                         <  2:548072/149‑1 (MQ=255)                                     aaaaGGGTGGGTGATCCCCT‑GCGCGTCCGGGAACGGGCCGCCGCGCGTCCCGAAC‑CCGTGGTGTACCCCAACCCGTAAAC‑CCCC‑TATCAGAATCATATAACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                       <  1:182767/151‑1 (MQ=255)                                     aaaaGGGGGAGTGTTTCCTG‑GCGCTTAGGGGACCGGGGCCCCGCGCG‑CCCGGAACCCGGGGTGTATCCCAAACCTTAAAC‑CCGC‑TATAAGGTTAAAAAAATCACCACCCCCCCCTGTGCCCGCCGTTACATCGTCGAAAACGATCTTaaa                                                                                                        <  1:1124156/150‑1 (MQ=255)                                       aaTGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACAt                                                                                                     >  2:299363/1‑151 (MQ=255)                                          ggtgggtgATTCCCT‑GCGCGTACGGGAACAGGTCGCCGCGCGTACGGGAC‑CGGGGGTGTATCTCGAACCGTAAAC‑CCGC‑TATCAGGATAATATGATCAACCCCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                                    <  2:722883/149‑1 (MQ=255)                                          ggggagtgaTCCCCG‑GCGCTTACTGTAACGGGCCGCCGCCCGGACGGAAA‑CCGGGGTGTACCAC‑AACCGGTAAACCCGC‑TAATAGAATTATATGAACACCCCCCGCGCCAAACCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                                    <  1:382835/146‑1 (MQ=255)                                               gtgaTTCCCT‑GCGCGTACTGGAACAGGTCGCCGAGCGTACCGGAA‑CCGTGGTGCATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                 >  2:581115/1‑147 (MQ=255)                                                   tccccT‑GCGCGTAGGGAAACGGGCGCCCGCGCTTACCGGAT‑CGGTGGTGTATCGCGACCCGTAAAC‑CCCT‑TAAAAGAACAATATAACAACCCCCCCCGCGGGTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                 <  2:679810/141‑1 (MQ=255)                                                   tccccG‑GCGCTTACGGGACCGGGCCCCCGCGCTTCCCGAAC‑CGGTGGTTTACCCCGACCCTTAAAC‑CCCC‑TATCAGGATAATATAACCACCCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                          <  1:729062/148‑1 (MQ=255)                                                     cccT‑GCGTTTACTGAAACGGGCCGCCCCGGTTCCCGGAC‑CCGGGGTTTATCCCGACCCTTAAAC‑CCGT‑TATCAGGATCATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCg                                                                                        <  2:329699/150‑1 (MQ=255)                                                     cccT‑GCGCTTACTGAACCAGGTCGCGGCGGGTCCGGGAA‑CGGTGGTTTATCCCGACCCTTAAAC‑CCGC‑TATCAGGATAATATAACAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCg                                                                                        <  2:171422/150‑1 (MQ=255)                                                             cgTACGGGAATGGGTCGCCGCGCGGCCGGGAC‑CCGGGTTTTCTCTGGACCGGTAAAC‑CCGT‑TATGGGGATCAAATGACCAGCCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                                  <  2:814535/149‑1 (MQ=255)                                                                  tGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                            >  2:178143/1‑150 (MQ=255)                                                                   ggAACAGGTCGCCGCGCGTCCCGGAC‑CCGTGGTTTATCTCGACCCGTAAAC‑CCGC‑TATCAGAATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                      <  2:47448/139‑1 (MQ=255)                                                                   gaaaCAGGTCGCCGCGCGTACTGGAA‑CGGTGGTTTATCTCGAACCTTTAAC‑CCTC‑TACCAGGATCATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                              <  2:588652/145‑1 (MQ=255)                                                                   gaaaCAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCAACCCTTTAAC‑CCGT‑TATAAGGATAATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                           <  2:180143/148‑1 (MQ=255)                                                                      aCAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                       >  1:181637/1‑151 (MQ=255)                                                                          gTCGCCGCGCGTCCCGGAA‑CCGTGGTGTACCTCGACCCTTTAAC‑CCGT‑TATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                       <  1:777837/147‑1 (MQ=255)                                                                           tCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                                  >  2:700155/1‑151 (MQ=255)                                                                              ccgcGCGTCCCGGAC‑CCGTGTTGTATCCCAAACCGTTAAC‑CCGC‑TATCAGGATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAata                                                                   <  2:680682/147‑1 (MQ=255)                                                                                gcgcgTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                               >  1:1073708/1‑149 (MQ=255)                                                                                gcgcgTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                               >  1:997412/1‑149 (MQ=255)                                                                                     tACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                            >  2:167953/1‑147 (MQ=255)                                                                                        cgggaccgggggtgTATCCCGACCCGTAAAC‑CCGC‑TATCAGGACCATATGACCACCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                      <  2:105748/141‑1 (MQ=255)                                                                                         cgcaccggtggtgTATCTCGACCTTTTAAC‑CCTT‑TAAAAGGACAATATAACCACCCCCCTCGCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                      <  1:252771/143‑1 (MQ=255)                                                                                          gAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                                   >  2:919013/1‑151 (MQ=255)                                                                                           aa‑CGGTGGTGTATCCGAAACCGTAAAC‑CCGC‑AATCAGGATAAAATGAACACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                  <  1:697574/151‑1 (MQ=255)                                                                                            accctggttttATCTCGAACCTTAAAC‑CCGC‑TATCGGGATAAAATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaa                                                              <  2:157648/129‑1 (MQ=255)                                                                                               cGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                               >  1:341401/1‑151 (MQ=255)                                                                                                gtgttttttctcGAACCGTAAAC‑CCCT‑TATCAGAATCATATAACCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                 <  1:867178/140‑1 (MQ=255)                                                                                                        tctcGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATTAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTg                                      >  1:961668/1‑151 (MQ=255)                                                                                                           cGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                                   >  2:195027/1‑151 (MQ=255)                                                                                                              aCCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                                >  1:728374/1‑151 (MQ=255)                                                                                                                     aaccccc‑TATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                          <  2:671689/145‑1 (MQ=255)                                                                                                                     aa‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                         >  2:949357/1‑151 (MQ=255)                                                                                                                         cGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                      >  2:593500/1‑151 (MQ=255)                                                                                                                             tATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGc                   >  2:868417/1‑151 (MQ=255)                                                                                                                              aTCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCt                  >  2:1132398/1‑151 (MQ=255)                                                                                                                                       atatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATATCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt         >  1:764446/1‑151 (MQ=255)                                                                                                                                              cAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATAtt  >  2:1119348/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                   CCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCT‑GCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATT  >  NC_000913/1376364‑1376651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑