Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	45.1%	78.3 / 14.3	51	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (24/4);  new base C (0/23);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.27e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376357‑1376652                                                                                                                                                         |                                                                                                                                                    cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACAcc                                                                                                                                                   >  2:188136/1‑151 (MQ=255)      cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                              <  2:1227086/151‑1 (MQ=255)             gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGc                                                                                                                                        <  1:952777/150‑1 (MQ=255)                cTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCACCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgc                                                                                                                                    >  2:287403/1‑151 (MQ=255)                         tAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                           >  2:399644/1‑151 (MQ=255)                               ggAGGGCGCCCGAAAAGGGGGGATTGTTCCCCGGCGCGTACGGGACCAGGTCCCCGC‑GCGTCCCGGAC‑CCGTGGTGTACCCCGAACCGTAAAA‑CC‑GTTATCAGGTCAATATGACCACCCCCCCCGCGGATGCCCGCCGTTACATCGTCGa                                                                                                                      <  2:964136/150‑1 (MQ=255)                                  cGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                  >  2:641444/1‑151 (MQ=255)                                        ccGAAAAAGGGTGAGTGTTCCCCTGCGCTTACTGGAACAGGCCGCCCC‑GCGT‑CCGGAACCCGGGGTGTATCCCGACCCTTAAAC‑CC‑GTTATCAGGATAATAGGATCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                              <  2:291339/149‑1 (MQ=255)                                        ccGAAAAAGGGTGAGTGATTCCCTGCGCGTCCGGGAACGGGCCGCCGC‑GCGTCCCGGAC‑GCGTGGTGTTTCTCGACCCGTTAAC‑CC‑GCTACCAGGATAATATGATCACCCCCCTCCCCGAGGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                            <  2:1174174/151‑1 (MQ=255)                                                        gaTTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                             >  1:403749/1‑150 (MQ=255)                                                        gaTTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                             >  1:990632/1‑150 (MQ=255)                                                         aTTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTa                                                                                            >  2:1092658/1‑150 (MQ=255)                                                          ttCCCTGCGCGTACTGGAACAGGTCGACGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAAGCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                           >  2:263068/1‑150 (MQ=255)                                                            cccTGCGCGTACTGGAACGGGTCGCCGC‑GCGTCCCGAAC‑CGGTGGTGTATCCCGACCCTTAAAA‑CC‑GCTACCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGa                                                                                               <  1:1099159/144‑1 (MQ=255)                                                                  gcgTACTGGAACAGGTCGCCGC‑GCGTCCCGGAC‑CCGTGGTGTATCTCGACCCTTTAAC‑CC‑GCTATCAGGATCATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                      <  1:1011685/147‑1 (MQ=255)                                                                   cgtgctgaactaGGTCGCCGG‑GCGTACCGGAA‑CGGTGGTGTACCTCTAACCCTTAAA‑CG‑CCTTTAAGAATCATAAAATCAACACCCCCGCCGCTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                                 <  1:1069759/140‑1 (MQ=255)                                                                     tACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                >  2:116533/1‑150 (MQ=255)                                                                      acgggAAAAGGTCGCGGC‑GCGTACCGGAA‑CCGTGGTGTATCTCAACCCGTTAAC‑CC‑GTTAACAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                                   <  1:1188211/143‑1 (MQ=255)                                                                       cggaaacgggcccccgc‑GCGTCCGGGAC‑CCGGGGTGTACCTCAACCCGTAAAC‑CC‑GCTATCAGAATCATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTAt                                                                              <  2:705345/137‑1 (MQ=255)                                                                       cTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                             >  1:764668/1‑151 (MQ=255)                                                                        tgaaaCGGGTCCCCGC‑GCTTCCCGGAA‑CCGGGTTTTATCTCCACCCTTTAAA‑CC‑GCTATCAGAATCATATGACCAACACCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTAt                                                                              <  1:1156175/146‑1 (MQ=255)                                                                         gaaaCAGGTCGCCGC‑GCGTCCGGGAC‑CCGTGGTGTATCTC‑AACCGGTAAACCC‑GCTACCAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                  <  1:834833/142‑1 (MQ=255)                                                                          taaCAGGTC‑CCGCGGCGTACCGGAC‑CCGGGTTGTACCTC‑AACCCTTAAACCC‑GCTATAAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                             <  2:78151/147‑1 (MQ=255)                                                                            acgggTCGCGGC‑GGGTCCCGAAC‑CGGGGGTTTCTCTCAAACCGTAAAC‑CC‑GCTATAAGAATAATATAAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                  <  2:869157/138‑1 (MQ=255)                                                                            aagagcccgcggggcgTCCGGGAA‑CGGTGTGTTATCGCGACCCGATAAA‑CC‑GCTATCAGGATCATAGTAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                           <  1:1199596/136‑1 (MQ=255)                                                                            aCAGGTCGCCGC‑GCGTACCGAAC‑CCGTGGTGTATCTCAACCCGTAAAC‑CC‑GCTATCAGGATAATATAATCAACCCCCTCCCCGATGCCCGCCGTTACATCGTCGAGAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                        <  2:285464/151‑1 (MQ=255)                                                                               ggTCGCCGC‑GCGTCCCGGAC‑CCGTGGTTTATCTCAACCCGTAAAA‑CC‑GATATCAGAATCATATGACCAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                      <  1:216829/150‑1 (MQ=255)                                                                                  cgccgc‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                  >  2:1143794/1‑151 (MQ=255)                                                                                      gc‑gcgTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                >  1:83909/1‑149 (MQ=255)                                                                                       c‑gcgTCCCGGAC‑CGGGGGTTTATCTCGAACCGTAAAC‑CC‑GCTATCAGGATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaag                                                              <  2:1136583/150‑1 (MQ=255)                                                                                           gTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                             >  1:470648/1‑148 (MQ=255)                                                                                                ggAC‑CCGGGGTGTATCTCGACCCGTAAAC‑CC‑GCTATCAGGATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                      <  1:1189998/150‑1 (MQ=255)                                                                                                   accggtggttTATCTC‑AACCCATAAA‑CCGGTTATAAAGATCTAATGAACAACCCCCGCGCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                      <  2:1125435/144‑1 (MQ=255)                                                                                                   accgggggttTATCTCAAACCGTAAAC‑CC‑GCTACCAGAATAATATGATCAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                   <  1:160267/145‑1 (MQ=255)                                                                                                   a‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                  >  2:1136628/1‑151 (MQ=255)                                                                                                     ccGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgc                                                 >  1:725320/1‑151 (MQ=255)                                                                                                          gtgtATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                            >  2:1210588/1‑151 (MQ=255)                                                                                                           tttttctcGACCCGTAAAC‑CC‑GTTATAAGAATAATATCATCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                            <  2:989447/146‑1 (MQ=255)                                                                                                            gtATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                           >  2:416117/1‑150 (MQ=255)                                                                                                              aTCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCt                                        >  1:994411/1‑151 (MQ=255)                                                                                                              aTCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCt                                        >  1:993384/1‑151 (MQ=255)                                                                                                              aTCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCt                                        >  2:91480/1‑151 (MQ=255)                                                                                                               tctcGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTg                                       >  1:563648/1‑151 (MQ=255)                                                                                                                    aaCCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                                   >  1:722561/1‑150 (MQ=255)                                                                                                                      ccGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                                 >  1:1108971/1‑150 (MQ=255)                                                                                                                            aaccc‑GCTATCAGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcg                            <  1:545151/147‑1 (MQ=255)                                                                                                                            aaccc‑GCAATAAGGATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACaa                               <  1:896185/144‑1 (MQ=255)                                                                                                                                c‑GCTATCAGGATAAAATAAACCACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                       <  2:764655/151‑1 (MQ=255)                                                                                                                                         ggATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGt               >  2:756388/1‑151 (MQ=255)                                                                                                                                         ggATCATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                 <  1:643898/149‑1 (MQ=255)                                                                                                                                         ggATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc                  <  1:479515/148‑1 (MQ=255)                                                                                                                                                       acacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTg  >  2:523414/1‑150 (MQ=255)                                                                                                                                                         |                                                                                                                                                    CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGC‑GCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CC‑GCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376357‑1376652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑