Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.1%	16.8 / 59.6	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/6);  new base A (0/24);  total (17/30)
Fisher's exact test for biased strand distribution p-value = 3.68e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.33e-05

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357742‑358033                                                                                                                                                      |                                                                                                                                                 gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCGTACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                                                 <  2:217570/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaaa                                                                                                                                              <  2:1237314/150‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                          >  1:892820/1‑151 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGACTCAATTCCGACAACAACCGCGCATTTATCCAACGCCCTGTTCAAAAATGCCTTCACCGCGGCCGCCAACCAGCTATTTTA‑TCGCCCCAACAAAAcc                                                                                                                                            >  2:949243/1‑148 (MQ=17)         tAGCGCATCAGGCAATTCCGGCCGCAGACCTGTGTCAGAGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCGTGTGCAAAAATGCCTTCGGGGCGGCTGTCTGCAAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                         <  2:1241092/150‑1 (MQ=255)          aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                                       >  1:933063/1‑151 (MQ=255)             gcATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCCGATACCGTGATTCATTTCCGCCAACACCCGCGCCTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                         <  2:311117/146‑1 (MQ=255)              cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                                                   >  1:1407406/1‑151 (MQ=255)               aTCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTATAGTT‑TATACCCAACAAAAcggccgcgc                                                                                                                                     >  2:1145147/1‑145 (MQ=14)               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctct                                                                                                                                  >  2:276987/1‑151 (MQ=255)                           cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                      >  2:1396181/1‑151 (MQ=255)                           cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                      >  2:479428/1‑151 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                     >  1:210205/1‑151 (MQ=255)                              ccacagccgtgtgtgAGCGGCTACCGTGTTTCATTCCCCCCAACCCCCGCCATTTTCCCCACCCCCATGTGAAAAAATCCCTTCGCGGGGGTTGTCTCCCATTTTTTTTT‑CCGCCGAAACAAAACCGCCGTTCTCTCCag                                                                                                                              <  2:609413/131‑1 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCCACAACCGCGCCTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                     >  1:931879/1‑149 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                   >  1:859220/1‑151 (MQ=255)                                     ccTGTGTCGGCGGCTACGGTGATTCATCCCCCCAAACACCCGCCCTTTTCCCCACCCCCATGTCCAAAAGTCCCTCGGCGGCGGCTGTCTCCCGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                               <  2:780292/148‑1 (MQ=255)                                     ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                   >  2:1098031/1‑144 (MQ=255)                                          gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcggaggaaaaa                                                                                                        >  2:495569/1‑140 (MQ=255)                                           tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggtagcggaaaa                                                                                                        >  2:1097572/1‑138 (MQ=255)                                            cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGaaaaa                                                                                                        >  1:703277/1‑146 (MQ=255)                                               cgcctcccttgcttCTTTCCCGCCAACACCCGCGCTTTTATCCAACGCCTGGTGAAAAAAGGCCTTCGGGGCGGTTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                                       <  2:1145411/134‑1 (MQ=255)                                                ggCTACCGTATTTCATTCCCCCAACCACCCGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTTCGCGGCGGTTGTCTGCCAGCTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                                   <  1:319738/149‑1 (MQ=255)                                                gcctccgttatttCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTAAAAAAATGCTTCCGGGGGGGCTGTCGGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                         <  1:762291/132‑1 (MQ=255)                                                gccacccttaattcattcCCCCCAACAACCGCGATTTTACCAACCGCCATGTAAAAAAATCCCTCCGCGGCGGCTGTCTGCAATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                            <  1:879377/130‑1 (MQ=255)                                                    aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGaaaaaaggttaaatc                                                                                              >  2:1370790/1‑138 (MQ=25)                                                     ccGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                                <  1:403947/147‑1 (MQ=255)                                                        tgtttCTTTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGGGGCGGCTTTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                                 <  1:1145486/140‑1 (MQ=25)                                                            tctttccccccAACACCCGCGCTTTTACCCAACGCCATGCAAAAAAAGCCCTTCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                       <  1:958698/140‑1 (MQ=255)                                                                       accacccGCGCTTTTACCCACCCCCATGGAAAAAAGTCCCTTCGGGGCGGTTTTCGGCCACTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                           <  1:67082/145‑1 (MQ=255)                                                                               cgcATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCcgtag                                                                                                                           >  2:1169958/1‑94 (MQ=255)                                                                                        caaacccttggtccAAAATTCCCTTGGCGGCGGCTTTCT‑CCAGGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                                        <  2:890783/138‑1 (MQ=255)                                                                                          acccccATGTAAAAAAATGCCTCCGCGGCGGTTGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTgg                                                      <  1:976498/147‑1 (MQ=255)                                                                                                      aaaacTTCCTGCGGGGGGGCTGTCTCCGAGTTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                             <  2:377359/148‑1 (MQ=255)                                                                                                      aaaaaTCCCTTCGCGGGGGCTGTCTCCCATCTTTTTCC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgc                                          <  1:1427178/151‑1 (MQ=255)                                                                                                      aaaaaGCCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                             <  1:306453/148‑1 (MQ=255)                                                                                                       aaaaTGCCTCCGCGGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                             <  1:661207/147‑1 (MQ=255)                                                                                                        aaaccccTGCGGGGCGTCTGTCTCCCAGTTTGTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                        <  2:684453/146‑1 (MQ=255)                                                                                                         aaTGCTTTCGCGGCGGCTGTCTCCCACCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcggc                                       <  1:724603/151‑1 (MQ=255)                                                                                                                    ggggccTGTCGCCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                    <  2:532563/138‑1 (MQ=255)                                                                                                                           tccTGCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                         <  2:932786/145‑1 (MQ=255)                                                                                                                            tcgcccAGTTTTTTTC‑CCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                        <  1:122750/143‑1 (MQ=255)                                                                                                                                ccAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                      <  1:1320434/145‑1 (MQ=255)                                                                                                                                  accttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                    <  1:1278447/140‑1 (MQ=255)                                                                                                                                     ttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa                <  1:1033569/144‑1 (MQ=255)                                                                                                                                     ttttttc‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt             <  2:536999/147‑1 (MQ=255)                                                                                                                                             ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg      <  1:591008/149‑1 (MQ=255)                                                                                                                                             ccgccaAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc       <  2:236042/148‑1 (MQ=255)                                                                                                                                                    aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAAACCCTCATGTTTTTGGGGGAACGCTGCTGGGGAAAAAATGGGAAAGGGAGGGGGGGGGAA‑CAACTCCAGAACCACGCCAAATGAGtttggccc  >  1:353313/1‑140 (MQ=255)                                                                                                                                                      |                                                                                                                                                 GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357742‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑