Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,487,1630CT42.6% 62.1 / 29.2 54intergenic (+200/‑72)hrpA/ydcFputative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (7/24);  new base T (23/0);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 2.69e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

GTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCG  >  NC_000913/1487014‑1487309
                                                                                                                                                      |                                                                                                                                                      
gTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTtcc                                                                                                                                                       <  2:1092420/151‑1 (MQ=255)
     ttattaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTcctcct                                                                                                                                                   <  1:806088/150‑1 (MQ=255)
         taATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAATAAGAATTCtttctttc                                                                                                                                                >  1:551653/1‑149 (MQ=255)
            ttCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAATAAGAATTTCTTCttttacag                                                                                                                                            >  1:290577/1‑145 (MQ=255)
             tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGTGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGt                                                                                                                                           <  1:141081/150‑1 (MQ=255)
             tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGt                                                                                                                                           <  1:1288167/150‑1 (MQ=255)
             tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAAAAAAACGAATTTCTCCcttttga                                                                                                                                             >  2:936665/1‑144 (MQ=255)
                  aaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCg                                                                                                                                     <  1:955410/151‑1 (MQ=255)
                            gTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGACATAAGAATTTTTCCTTTTAGAGTGGTCCCCTtctctc                                                                                                                             >  1:306417/1‑147 (MQ=255)
                              aaaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGGAAAACCGCTTCCTCCTTTTATATTGCGCCGCTTTTTACtatt                                                                                                                         >  2:286218/1‑151 (MQ=255)
                              aaaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACtatt                                                                                                                         <  2:1265226/151‑1 (MQ=255)
                                aaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACtattat                                                                                                                       <  1:1018637/151‑1 (MQ=255)
                                 aaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTAtc                                                                                                                      <  2:763617/151‑1 (MQ=255)
                                    tCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATAAGATTTTCTCCTTTTCTAGGGCTCCCCTTCTCACtattattt                                                                                                                     >  2:562545/1‑147 (MQ=255)
                                    tCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAAAAAATTTCTCCTTTCTTAGTGGTCCGCCTCTCCCTATTTtct                                                                                                                     >  1:833892/1‑149 (MQ=255)
                                      aGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACg                                                                                                                 <  1:11273/151‑1 (MQ=255)
                                        gAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTATGACATAAAAATTTCTCCTTTTACAGTGGTTCGCCTCTCCCtatt                                                                                                                         >  1:1246137/1‑141 (MQ=255)
                                              aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGCTATGGAAAAAAAATTTTCTCCTTTTCATGAGCGCCGCCTTTCCCTATTATATCAcccgggatt                                                                                                          >  2:552225/1‑142 (MQ=255)
                                                aaaaaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAATAAGATTTTCTCCTTTTTGAGGGGTCCGCCTCTCCCTATTATTTCTCCCAGTATtttt                                                                                                     >  2:601112/1‑151 (MQ=255)
                                                aaaaaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACAAATTTCTCCTTTTAGAGTGCCCCCCTTCTCACTATTATTTTACTCAGTATtttt                                                                                                     >  2:37194/1‑151 (MQ=255)
                                                aaaaaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCtt                                                                                                     <  1:468256/151‑1 (MQ=255)
                                                        aaTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAAc                                                                                             <  1:337478/151‑1 (MQ=255)
                                                            ctctGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAATACAATTTTCTCCTTTTTGAGTGGTCCGCTTCTCACTATTTTTTCACGCCGGATTTTTTAggggaag                                                                                            >  1:505684/1‑144 (MQ=255)
                                                              ctgctgCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATa                                                                                         <  1:900875/149‑1 (MQ=255)
                                                                gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAagg                                                                                      <  1:471968/150‑1 (MQ=255)
                                                                  tgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGACATAAGATTTTCTCCTTTTTGAGTGCTCCGCCTCTCCCTCTTTTTTCACCCAGGATTCTTTAGGGGACGATaa                                                                                        >  1:979727/1‑146 (MQ=255)
                                                                   gcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAaggagg                                                                                   <  2:378911/150‑1 (MQ=255)
                                                                    cAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGaa                                                                                 <  1:45243/151‑1 (MQ=255)
                                                                    cAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGaa                                                                                 <  2:1135511/151‑1 (MQ=255)
                                                                      aGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGACATAAGAATTTCTCCTTTCAGAGTGCTCCGCCTCTCACTATTATTTCACCCCGGATTCTTTAAGGGACGATAaagaggga                                                                                 >  2:854618/1‑147 (MQ=255)
                                                                        aTGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCAt                                                                             <  2:841129/151‑1 (MQ=255)
                                                                          gAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATg                                                                           <  1:318997/150‑1 (MQ=255)
                                                                             taatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAGATTTTCTCCTTTTTGAGTGCTCCCCCTCTCACTATTATTTCACCCAGGATTTTTTAAGGAACGAAAAAGAGGAAACATGaaa                                                                        >  2:1161016/1‑149 (MQ=255)
                                                                              aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACAt                                                                     <  1:905057/151‑1 (MQ=255)
                                                                              aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACAt                                                                     <  2:82725/151‑1 (MQ=255)
                                                                               atGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATAAAATTTTCTCCTTTTTTAGGGCTCCGCCTCTCACTCTTATTTCACCCCGGATTTTTTATGGAAAGGTAAAGAGGAAACAAGAAAAtt                                                                    >  1:1192402/1‑151 (MQ=255)
                                                                                 gTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTa                                                                   <  1:178504/150‑1 (MQ=255)
                                                                                         aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGACATAACATTTTCTCCCTTTCTAGTGGTCCGCCTTTCCCTATTTTTTCACCCAGAATTTTTTTGGGGAAGATAAAGAGGGAACATGAAAAATAaccccctt                                                           >  1:1199135/1‑146 (MQ=255)
                                                                                             cATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAAATTTCCTCCCTTTAGAGGGCTCCGCCTTTCTCTATTATTTCACCCAGTATTTTTTAAGGGAAGAAAAAGAGGAAACAAGAAAATTATCCCCttttc                                                         >  2:1253053/1‑146 (MQ=255)
                                                                                              aTTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAACATTTTCTCCTTTTCGTGGGGTTCGCCTCTCCCTATTTTTTTACCCAGTATTTTTTATGGGAAGATAAGGAGGGAACATAGAAAATACCCCCCTTTcccc                                                       >  1:8532/1‑148 (MQ=255)
                                                                                              aTTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGATTAAGAAATACAATTTTCTTCTTTTTGAGTGGTCCGCCTCTCACTCTTTTCTCTCGCACGATTTTTTTAGGAACGATAAGGGGGGAACATAAAAAATAACCCCCTTCCgcc                                                      >  1:917413/1‑148 (MQ=255)
                                                                                                  ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATACGAATTTTTCCTTTTTTGGTGGTCCCCCTCTCCCTATTATTTCCCCCCGTATTTTTTAGGGGAAGGTAAAGAGGGAACAAGAAAAATAACCCCTTTTCGACGCttt                                                 >  1:209332/1‑151 (MQ=255)
                                                                                                   cTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGAAATAAAATTTTCTCCTTTTTGAGGGGTCCGCCTCTCACTATTTTTTTCCCCCGTATTTTTTAGGGGAAGATAAAGGGGGACCATGAAAAATACCCCCttttccccccctt                                                 >  1:30673/1‑140 (MQ=255)
                                                                                                    ttAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATACGATTTTCTCCTTTTAGAGGGTTCCCCCTCTCCCTATTTTTTCACCCAGTATTTTTTAAGGGAAGAAAAAGAGGAAACATGAAAATTAcccccctttccacgcctt                                                 >  2:1211444/1‑135 (MQ=255)
                                                                                                         aGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAACGATTTTCTCCTTTTTGAGGGGTCCCCTTTTCACTATTTTTTTACCCAGGATTTTTTAAGGGAAGATAAAGAGGAAACATGAAAAATAACCCCCTTTCGACGCcttttcc                                             >  2:364548/1‑144 (MQ=255)
                                                                                                            tatGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAACATTTTCTCCTTTTCGAGGGCTCCCCCTTTCCCTTTTTTCTCACGCAGGAATTTTTTAGGGAAGAGAAAGAGGGAACAAAAAAAATAACCCGCTTTCGACCCtttttcc                                             >  1:1047432/1‑141 (MQ=255)
                                                                                                                 cAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAg                                  <  1:881200/151‑1 (MQ=255)
                                                                                                                      ttGCGGAGTGGCGGTTAAGGAAATAAGAATTTCTCCCTTTTTAGGGTTCCCCTTCTCACTATTTTTTCACGCAGTATTTTTTATGGGACGATAAAGAGGGAACAAGAACATTTACCCCGTTCCCCCGCCTTTGCCCGGAACtataaaaggc                             >  1:621830/1‑145 (MQ=255)
                                                                                                                        gCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCa                            <  2:1193445/150‑1 (MQ=255)
                                                                                                                                gCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGtt                    >  1:1240084/1‑150 (MQ=255)
                                                                                                                                           aCATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtg         <  2:1184710/151‑1 (MQ=255)
                                                                                                                                           aCATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtg         >  2:301079/1‑151 (MQ=255)
                                                                                                                                                cGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtggctgg    >  1:1165557/1‑151 (MQ=255)
                                                                                                                                                 gATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtggctggc   <  2:503629/151‑1 (MQ=255)
                                                                                                                                                 gATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtggctggc   >  1:124511/1‑151 (MQ=255)
                                                                                                                                                  aTTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGgcg  <  1:936533/151‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                      
GTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCG  >  NC_000913/1487014‑1487309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: