Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	64.9%	1.6 / 27.5	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (8/5);  new base A (0/24);  total (8/29)
Fisher's exact test for biased strand distribution p-value = 3.33e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-03

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357741‑358036                                                                                                                                                       |                                                                                                                                                   tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                    >  2:531894/1‑150 (MQ=255)    tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                                 >  1:660100/1‑150 (MQ=255)       gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                                             <  1:860580/151‑1 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                            >  1:389379/1‑151 (MQ=255)                          tccctccgccgCCCTGTGTCCGCGGCTACCGTGATTCATTTCCGCCAACACCCGCGCATTTCTCCAACGCCCTGTGCCCAACTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACACAACCGCCGGTCTCTCCAGTAGTgg                                                                                                                          >  2:825005/6‑151 (MQ=255)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                          >  2:936863/1‑151 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                        >  1:550081/1‑151 (MQ=255)                                cGCAGCCTTGTGTCGGCGGCTACGGTGATTCATTCCCCCCAACCCCCGCGCATTTATCCAACCCCTTGTAAAAAAATGCCTTCGCGGCGGCTGTGTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                     <  1:321771/150‑1 (MQ=255)                                   agcccTGTGCCAGCGCCTCCGGTTTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATGCTTTCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                                   <  1:930493/146‑1 (MQ=255)                                      ctggtgcCAGGGTCTACCGTGTTTCTTTCCCCCAAACACCCGCCCATTTACCCAACGCCTTGTGAAAAAATCCCTTCGGGGCGGCTGTCGCCCAGCTTTTTTT‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                                <  2:828862/146‑1 (MQ=255)                                                cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGCGGGAGaaaaaaacttt                                                                                                    >  1:436179/1‑143 (MQ=25)                                                cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCCATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGccaagaaaaggac                                                                                                        >  2:251556/1‑135 (MQ=255)                                                      ccgtttttCTTTCCCCCCAACAACCGCGCATTTCTCCACCCCTGTGTCAAAAAATGCCTTCGCGGCGGCTGTCCCCCAGTTTTTTTT‑CCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                                  <  2:852710/141‑1 (MQ=255)                                                      ccGTGTTTCATTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                                   <  2:394079/146‑1 (MQ=25)                                                      ccGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGGGAAAAAATGCCTTCGGGGCGGCTGTCTCCCAGCTATTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                                <  2:87903/149‑1 (MQ=255)                                                            ttCTTTCCCGCCAACACCCGCGATTTTACCCACCGCCATGTAAAAAAATGCCTTCGCGGGGGCTGTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                                           <  2:1045043/148‑1 (MQ=255)                                                                 tcccGCCACCACCCGCCCATTTACCCACCCCCTTGGAAAAAAATCCCTCCGGGGGGGTTGCCTGCCGGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                     <  1:673021/147‑1 (MQ=255)                                                                  ccccccAACCCCCGCGCATTTACCCACCGCATTGGAAAAAAGTGCCTCCGGGGGGGTTGCCTGCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                                          <  1:432774/139‑1 (MQ=255)                                                                   cccccAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAAATCCCTCCGCGGCGGTTTTCGCCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                            <  1:942141/137‑1 (MQ=255)                                                                             ccGCGTTTTTACCCACCCCCATGTGAAAAAATGCCTTCGCGGCGTCTGTCTCCCAGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                       <  1:118528/151‑1 (MQ=255)                                                                               gcgcTTTTCCCCACCGCCATGTGAAAAAATCCTTGCGCGGCGTCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                      <  1:878699/150‑1 (MQ=255)                                                                               gcccttttCTCCACCGCCAGTTGAAAAAAGCCCTCCGCGCCGGCTTTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                         <  1:639690/142‑1 (MQ=255)                                                                                           aaCGCCATGTGAAAAATTGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                          <  2:304770/150‑1 (MQ=255)                                                                                            accctaTGTACAAAAAGGCCTCCGCGGCGGCTTTCTGCCATCTATTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                        <  1:570065/146‑1 (MQ=255)                                                                                               catttggaaaaaaTGCCTGCGGGGGGGCTGTCCGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                          <  1:903764/138‑1 (MQ=255)                                                                                                       aaaaaTGCCTCGCCGGGGGCTTTCT‑CCAGGTTTTTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                    <  1:599695/144‑1 (MQ=255)                                                                                                       aaaaaGCCCTCCGCGGCGGCTTTCGCCCGGTTTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                             <  2:715029/151‑1 (MQ=255)                                                                                                        aaagtcccTCCGGGGGGGCGGTCTCCCTGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                            <  1:764350/145‑1 (MQ=255)                                                                                                           agccttccggggcggtTCTCTCCCTGTTTTTTTC‑CCCCCGAAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                          <  1:466095/140‑1 (MQ=255)                                                                                                               ctccggggcggcTTTCTGCCAGTTTTTTTC‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                        <  1:618512/142‑1 (MQ=255)                                                                                                                   ggggcggcTGTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                    <  2:295477/146‑1 (MQ=255)                                                                                                                         gcTGTCTGCAGGTTTTTTTC‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                              <  1:542714/148‑1 (MQ=255)                                                                                                                            gTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                         <  1:945116/150‑1 (MQ=255)                                                                                                                              cTGCCTCCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                        <  1:192729/149‑1 (MQ=255)                                                                                                                                   aGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa                  <  2:113316/150‑1 (MQ=255)                                                                                                                                    gttATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                <  2:969388/149‑1 (MQ=255)                                                                                                                                      ttttttc‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                       <  1:306391/140‑1 (MQ=255)                                                                                                                                              ccgccgCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAACTTTTAACCCCCCCTGTTTTGTGGGGATCGCTGCTGGGGAAAAAATGGGAAGGGGAGGGGGGGGGGACAGCTCCACAACCGCGCCAAttttggtt          >  2:240828/1‑142 (MQ=255)                                                                                                                                                     aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAGCTTTTAAACCCCCCTTTTGTGTGGGGAACGCCGCTGGTAACAATGTGGGAAGGGGAGGGGGGGGGAAGAACTCCCCCACCGCGCCAATTAAGGTTGCCTc     >  2:47748/1‑146 (MQ=255)                                                                                                                                                      acaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt  <  1:955826/148‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357741‑358036

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑