Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,561,018 C→A 19.3% intergenic (+120/‑350) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,561,0180CA19.3% 82.6 / 2.2 49intergenic (+120/‑350)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (23/15);  new base A (9/2);  total (32/17)
Fisher's exact test for biased strand distribution p-value = 2.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTG  >  NC_000913/2560875‑2561165
                                                                                                                                               |                                                                                                                                                   
ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTAGCATTTTAGGAGTGTGAATAGTTGACATTaa                                                                                                                                                >  1:679612/1‑149 (MQ=255)
         tACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGGAGTTAAGGTGGGTCa                                                                                                                                       >  1:365935/1‑149 (MQ=255)
            aacaTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGGGGGTCAAAAGTTGCCGTTTAGGTGTGTGAAAAGTTGAAGTTAAGGTGTGTCtaaa                                                                                                                                    >  1:134145/1‑149 (MQ=255)
                         ggAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGACGTTAAGGTGGGTCAAAAGTTGCCGAGTAAg                                                                                                                       >  2:1389646/1‑149 (MQ=255)
                         ggAATCAGGCGGGCAATGTTCCCGCCATTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGTGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCAGTTAAGGAGGGTCAAAATTTGCCAAGTAAg                                                                                                                       >  2:743580/1‑149 (MQ=37)
                             tCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGTTGGGTCAAAAGTTGCCGTTAAGGAGGGTCAAAAGTTGCCGTTAAGGGGGGTCAAAATTTTACGAGTAACAAtt                                                                                                                   >  1:146213/1‑149 (MQ=38)
                                ggCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGTTGGGTAAAAAGTTGCCTTAAAGGTGGATCAAAAGTTGAAGAAAAGGTGGGTGAAATATTGCAGAGAAAGAATTgta                                                                                                                >  2:1424372/1‑149 (MQ=255)
                                     gCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGGTAAGGAGAGTAAAAATTTGCATTTAAGGTGTGGCAAAATTTGCAGAGTAAGAATAATACTAtt                                                                                                           >  1:578958/1‑149 (MQ=255)
                                               cGCCTTTTCTTTGCCTCAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAATTTGCCGTTAAGGAGGGTCAAAATTTGAAGTAAAGGTGGGTCTAAAGTTGCAGAGAAAGAATTGTACAATTAAGATTTcaa                                                                                                 >  2:1502894/1‑147 (MQ=25)
                                                   ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTTAGGTGGGGCAAAATTTGCAGAGTAAGAATTCTACTATTAATAATTCTAGGCg                                                                                             >  2:1336808/1‑149 (MQ=37)
                                                           gCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGTGTAAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCAGTAAAGGTGTGTCTAATTGTGACGAGTAAGAATTCTACAATTAAAAATAATACGCGACGGGAGt                                                                                     >  2:344223/1‑149 (MQ=21)
                                                            ccTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCAGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGAAGtt                                                                                    >  1:1374102/1‑149 (MQ=255)
                                                              atAAATCCATGAATTCAGTCGCGAACAAATTAGGCATTACTGGTGGCTAAAAAGCAGCCTTTAAGGTGGGTCAAAAGTAGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGtttt                                                                                  <  2:407184/148‑1 (MQ=21)
                                                               tAAATCCATGAATTCAGCTGGGTAAAAAGTAGCCCTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGttttt                                                                                 <  2:500623/149‑1 (MQ=37)
                                                                 aaaccATGAAATCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTAGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGGGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTa                                                                               <  1:1033838/146‑1 (MQ=255)
                                                                  ttCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCAGTAAAGGTGGGTCAAAATTTGCCGAGTAATAATTCTACAATAAATAATTCTACGCGACGGGATTTTTTAAg                                                                              >  2:43696/1‑149 (MQ=25)
                                                                  ttCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTGAAGGTGGGTGAAAATTTGGCGTTAAGGTGGCGGAAAATTTGAATAGTAAGAATTATAAAATTAATATTAGTAAGCGTCGTGAttttttatg                                                                              >  2:303114/1‑146 (MQ=16)
                                                                  ttCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAAGTTGCCGTTAAGGAGTGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGACGAGTAAGAATTCTACTATTAAGAATTCTAAGCGACGTGAGTTTTTTAg                                                                              >  1:1102472/1‑149 (MQ=38)
                                                                  atCCATGCATTCAGGGGGGTAAAAATTAGCCCTTAGCGGTGGCTCAAAAGCAGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                                                              <  1:700710/148‑1 (MQ=37)
                                                                      aTGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTGAAAATTTGCATAGTAAGAATTCTACAATTAAGAATTATACGCGACGGTATTTTTTTAGACta                                                                          >  1:953789/1‑148 (MQ=25)
                                                                       tGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGTGTAAAAATTTGCAGTTAAGGAGACTCAAAAGTTGAAGAAAAGGTGTGTCAAAATTTGAAGAGAAAGAATTATAATATTAAGAATTATACGCGTCGGGATTTTTTTAGACtaa                                                                         >  2:368041/1‑147 (MQ=16)
                                                                       tGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGGGTAAAAAGTTGCCGTTAAGGTGAGTCAAAATTTGCCGTGAAGGGGGGTCAAAAGTTGACTAGTAAGAATTGTAATTTTAATATTTATAAGCGTCGTGAGTTTTTTAGACtta                                                                         >  2:1085298/1‑147 (MQ=18)
                                                                          aTTCATTTGGGTAAAAAGTAGCCTTTCGTGTGGGGTCTATACCTGCCTTTTCGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCcgg                                                                      <  1:828903/149‑1 (MQ=25)
                                                                                     tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTAGCCGTTAAGGTGGGGCAAAAGTTTAATAGTAAGAATTCTACAATTAACAATAAAATGAGACGGGAGTTTATTATCCTCAAGGTCCTTCATaca                                                           >  2:98543/1‑147 (MQ=16)
                                                                                     tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                                                           >  1:547222/1‑149 (MQ=255)
                                                                                     tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCAGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGACTCCCGGTCGGTCATaga                                                           >  2:1280203/1‑149 (MQ=255)
                                                                                        aaaGTTGCCGTTAGTGGTGGGTCAAAAGTTTCAGTTAAGGTGGTTCAAAAGTTGCCGTTAAGGTGTGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACTGGAGTTTTTTATCATCCCGGTCGGTAATagagag                                                        >  1:1123241/1‑149 (MQ=38)
                                                                                               cccttAGTGGGGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTa                                                 <  2:1288988/146‑1 (MQ=255)
                                                                                               ccGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTa                                                 >  1:894895/1‑149 (MQ=255)
                                                                                                    tgtggggGGTCAAAAGTGGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                                            <  1:524959/148‑1 (MQ=255)
                                                                                                          gggTAAAAAGTTGCCGTTAAGGTGGGTAAAAAGTTTCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAAATCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag                                      <  1:359224/149‑1 (MQ=255)
                                                                                                            gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTATACTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaa                                    >  1:1316643/1‑149 (MQ=255)
                                                                                                            gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaa                                    >  1:1310630/1‑149 (MQ=255)
                                                                                                             tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCTCCTAGAGTTAAACagaaa                                   >  1:366755/1‑148 (MQ=255)
                                                                                                             tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaat                                   >  2:527779/1‑148 (MQ=255)
                                                                                                                 aaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGTAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAatt                               >  1:133430/1‑149 (MQ=255)
                                                                                                                    ttGCCGTTAAGGTGGGGCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattatt                            <  1:1566353/149‑1 (MQ=255)
                                                                                                                         ttttatgTGGGTCAAATGTTGCCGGTCAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCTACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTcgcc                       <  1:1143463/143‑1 (MQ=255)
                                                                                                                          ttAAGGTGGGTCAAAAGCTGCAGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTcgccg                      <  1:265021/149‑1 (MQ=255)
                                                                                                                             tggTGGGTAAATAGTTGCAGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAATAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCt                   <  2:1583992/148‑1 (MQ=255)
                                                                                                                             atgTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCt                   <  1:1502894/147‑1 (MQ=255)
                                                                                                                                tGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGAt                <  2:365935/149‑1 (MQ=255)
                                                                                                                                  ggTCAAAAGTTGCCGTTATGGTGTGTCAAAATTTGCAGAGTAAGAATTCTACTATTAAGAATTCTAGGCGAGGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAg              <  2:578958/149‑1 (MQ=255)
                                                                                                                                    tCAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGt            <  2:134145/149‑1 (MQ=255)
                                                                                                                                    tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGt            >  1:763224/1‑149 (MQ=255)
                                                                                                                                    tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGt            >  2:58229/1‑149 (MQ=255)
                                                                                                                                    tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGt            >  1:571829/1‑149 (MQ=255)
                                                                                                                                      aaaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCg          >  1:773465/1‑149 (MQ=255)
                                                                                                                                        aaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGc        <  1:1554344/149‑1 (MQ=255)
                                                                                                                                              ccGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGGCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTg  <  1:3572/149‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
TTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTG  >  NC_000913/2560875‑2561165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑