Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA56.7% 12.4 / 38.6 30L267F (TTG→TTTcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (8/5);  new base A (0/17);  total (8/22)
Fisher's exact test for biased strand distribution p-value = 2.20e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.64e-04

GCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357747‑358032
                                                                                                                                                  |                                                                                                                                               
gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                          >  1:362792/1‑151 (MQ=255)
  gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                         <  1:433418/150‑1 (MQ=255)
      cccATCAGCCAATCCCAGCCCCAGACCTGTTTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAATTGCCTCGGCGGCGGCTGTCTGCCAGTTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                       <  2:8652/146‑1 (MQ=18)
           cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                               >  1:689215/1‑151 (MQ=255)
                      aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                    >  2:455066/1‑151 (MQ=255)
                       gCCCCACACTTGTGTCTGCGCCTCCCGTAATTATTTCCCCCAAACAGCCGCCCTTTTTCCCACCTCAATGTAAAAAAATCCTTGCGGGGGGGTTGTCGCCCGGTTTTTTCCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                      <  1:131827/148‑1 (MQ=255)
                         cGCAGCCTTGTGTCAGGGCCTACCGTGTTTCATTCCCCCCAACACCCGCGCATTTACCCACCGCCTTGTCAAAAAATGCTTGCGGGGGGGCTGTCTGCCGGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                 <  1:73522/151‑1 (MQ=255)
                           cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  2:923837/1‑148 (MQ=255)
                               cgtgtgTCAGCGGCTCCGGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAGGCTTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                              <  1:558397/146‑1 (MQ=255)
                                    gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  2:468941/1‑139 (MQ=255)
                                    gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAaggg                                                                                                            >  1:270815/1‑143 (MQ=255)
                                                cctttattctttCCCCCAACCACCCGCCCATTTACCCACCCCCTGGGGAAAAAATCCCTCGGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                               <  2:837379/122‑1 (MQ=255)
                                                     ttCATTCCCCCCAACACCCGCGCTTTTACCCACCGCATTGTGAAAAAATGCTTCCGGGGCGCCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                                       <  1:922392/148‑1 (MQ=255)
                                                       ctttccccccAACACCCGCGTTTTTACCCACCCCCATGGGAAAAATTCCCTTCGCGGCGGTTGTCTCCAGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                                      <  1:267735/139‑1 (MQ=255)
                                                           ccccccAACACCCGCCATTTTACCCACCGCCTTGTCAAAAAATGCCTCGGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                              <  1:1278190/147‑1 (MQ=255)
                                                                  aacaccCGCCCATTTACCCACCCCCATGTAAAAAAAGGCTTCCGGGGCGGCTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                        <  1:896938/151‑1 (MQ=255)
                                                                          gcgcTTTTACCAAACCCTATGTAAAAAAATCCTTGCGCGGGGGCTGTCTGCCAGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                    <  1:1196114/148‑1 (MQ=255)
                                                                                    caaacccgtgggcaaaaaaTGCCTCCGGGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                         <  2:1323813/135‑1 (MQ=255)
                                                                                      accgcttgggacAAAAATGCCTCGGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                     <  2:187722/140‑1 (MQ=255)
                                                                                              gtgAAAAAATCCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                               <  2:979972/149‑1 (MQ=255)
                                                                                              ggcaaaaaaTGCCTCCGCGGGGGTTGCCGGCGAGTTTTTTCCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                             <  2:310983/147‑1 (MQ=255)
                                                                                                  aaaatTGCCTCCGCGCGGGCTTTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                             <  1:79548/147‑1 (MQ=255)
                                                                                                   aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAGTTTAAAACCCTCAATGTTTTTGGGGATAGCTGCTGGTTACAACGTgg                                                     >  2:783339/1‑138 (MQ=255)
                                                                                                    aattGCCTCCGGGGCGCCTTTCCGCCGTTTTTTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                       <  2:24848/148‑1 (MQ=255)
                                                                                                                ggcggtTGTCTCCCGCTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                  <  2:1329885/144‑1 (MQ=255)
                                                                                                                     cTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTAAACCCCCATGTTTTGTGGGGAACGCTGCCGGGGACAAAATGGGAAGGGGAGGGCGGGGGAACAACTCCCGaa                       >  1:1253634/1‑150 (MQ=255)
                                                                                                                            ccAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                  <  1:506326/148‑1 (MQ=255)
                                                                                                                                 ttttttcCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt            <  1:1153583/147‑1 (MQ=255)
                                                                                                                                      ttcccgccgCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAACGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt       <  1:810575/147‑1 (MQ=255)
                                                                                                                                          ccccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  1:19340/149‑1 (MQ=255)
                                                                                                                                                aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAAACCCCCCTGTTTTTTGGGGATCGCCGCTGGGAAAAAAATGGGAAGGGGAGGGGGGGGGAGCAGCTCCCGAAACGCGCCAAATTAGttt      >  1:1158706/1‑140 (MQ=255)
                                                                                                                                                  |                                                                                                                                               
GCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357747‑358032

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: