Predicted mutation
evidence seq id position mutation freq annotation gene description
RA BX571857 425,660 T→C 12.9% S144P (TCA→CCA)  SAS0381 → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*BX571857425,6600TC12.9% 215.9 / 20.4 62S144P (TCA→CCA) SAS0381conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (36/18);  new base C (3/5);  total (39/23)
Fisher's exact test for biased strand distribution p-value = 1.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.30e-01

TATTCAGTTGAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAATAGCTGGT  >  BX571857/425564‑425755
                                                                                                |                                                                                               
tATTCAGTTGAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTAt                                                                                                 <  2:781960/97‑1 (MQ=255)
   tCAGTTGAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCAt                                                                                              >  1:1459369/1‑97 (MQ=255)
      gTTGAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTac                                                                                           <  2:1003783/97‑1 (MQ=255)
         gAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTacaac                                                                                        >  2:755257/1‑97 (MQ=255)
          agtACAACTTAAGATACCCTATTACAAAAAAATTCTTAAATGGAGGTATCGTTTTAAATGATTTGAAAGAAAAAAATTTTTCCCTATCATTacaaca                                                                                       <  2:93056/95‑1 (MQ=255)
            tACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACaaa                                                                                     >  1:1004785/1‑97 (MQ=255)
            tACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACaaa                                                                                     >  1:481979/1‑97 (MQ=255)
             aCAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACaaaa                                                                                    >  2:319418/1‑97 (MQ=255)
             aCAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACaaaa                                                                                    >  2:1433610/1‑97 (MQ=255)
              cAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACtaaaa                                                                                   >  1:1345425/1‑97 (MQ=255)
               aaCTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAg                                                                                  <  1:288574/97‑1 (MQ=255)
                aCTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAgg                                                                                 >  1:1291565/1‑97 (MQ=255)
                aCTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAgg                                                                                 >  1:1562401/1‑97 (MQ=255)
                aCTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAgg                                                                                 <  1:1360460/97‑1 (MQ=255)
                         aCTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGatat                                                                        >  2:458831/1‑97 (MQ=255)
                            ctATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGaa                                                                     >  1:808636/1‑97 (MQ=255)
                              aTTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAGGTGTTGATATGaaaa                                                                   <  2:1034372/97‑1 (MQ=255)
                                tACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATa                                                                 >  1:1289785/1‑97 (MQ=255)
                                tACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATa                                                                 >  1:685982/1‑97 (MQ=255)
                                 aCAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAg                                                                >  2:253630/1‑97 (MQ=255)
                                          ttattaAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACa                                                       >  1:1277956/1‑97 (MQ=255)
                                           tattaAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACAt                                                      >  1:1200053/1‑97 (MQ=255)
                                            attaAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATa                                                     >  1:1192414/1‑97 (MQ=255)
                                             ttaAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAg                                                    <  2:845050/97‑1 (MQ=255)
                                                aaTGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCtt                                                 >  1:1245653/1‑97 (MQ=255)
                                                   ggAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCTCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCAt                                              >  2:642128/1‑97 (MQ=255)
                                                      aGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTAt                                           <  1:691839/97‑1 (MQ=255)
                                                      aGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTAt                                           <  1:692009/97‑1 (MQ=255)
                                                       gTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATc                                          <  2:1082692/97‑1 (MQ=255)
                                                        tATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCa                                         <  2:902489/97‑1 (MQ=255)
                                                          tCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCAtt                                       <  2:784467/97‑1 (MQ=255)
                                                            gATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTa                                     <  2:443650/97‑1 (MQ=255)
                                                              tttAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTaaa                                   >  1:1285918/1‑97 (MQ=255)
                                                               ttAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAAc                                  <  1:979899/97‑1 (MQ=255)
                                                               ttAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAAc                                  >  1:743572/1‑97 (MQ=255)
                                                                tAAATGATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACa                                 <  2:1007754/97‑1 (MQ=255)
                                                                  aaTGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATc                               <  2:304059/97‑1 (MQ=255)
                                                                    tGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCaa                             <  2:713458/97‑1 (MQ=255)
                                                                    tGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCaa                             >  2:1056297/1‑97 (MQ=255)
                                                                    tGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCaa                             >  2:569483/1‑97 (MQ=255)
                                                                    tGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCaa                             >  2:1545684/1‑97 (MQ=255)
                                                                     gATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAg                            >  1:580500/1‑97 (MQ=255)
                                                                     gATTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAg                            >  2:639889/1‑97 (MQ=255)
                                                                      aTTTGAAAGAAAAAGATTTTTCCCTACCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGt                           <  1:565470/97‑1 (MQ=255)
                                                                       tttGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTa                          >  1:811790/1‑97 (MQ=255)
                                                                         tGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGa                        >  2:1448149/1‑97 (MQ=255)
                                                                         tGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGa                        >  1:154958/1‑97 (MQ=255)
                                                                         tGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGa                        >  1:155034/1‑97 (MQ=255)
                                                                         tGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGa                        >  1:779698/1‑97 (MQ=255)
                                                                         tGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGa                        >  1:253616/1‑97 (MQ=255)
                                                                                 aaaGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAatta                >  1:375950/1‑97 (MQ=255)
                                                                                   aGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAattatt              >  1:331512/1‑97 (MQ=255)
                                                                                    gATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTAttt             >  1:559407/1‑97 (MQ=255)
                                                                                    gATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTAttt             >  1:1251849/1‑97 (MQ=255)
                                                                                    gATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTAttt             <  2:806386/97‑1 (MQ=255)
                                                                                     aTTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTAtttt            <  1:1378380/97‑1 (MQ=255)
                                                                                     aTTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTAtttt            <  1:151126/97‑1 (MQ=255)
                                                                                       ttttCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTaa          <  1:1323431/97‑1 (MQ=255)
                                                                                        tttCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAAt         >  1:222765/1‑97 (MQ=255)
                                                                                        tttCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAAt         >  1:927152/1‑97 (MQ=255)
                                                                                            ccTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAATAGCt     >  2:1535617/1‑97 (MQ=255)
                                                                                               aTCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAATAGCTGGt  <  2:785408/97‑1 (MQ=255)
                                                                                               aTCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAATAGCTGGt  <  2:1184274/97‑1 (MQ=255)
                                                                                                |                                                                                               
TATTCAGTTGAATACAACTTAAAATACTCTATTACAAAAAAATTATTAAATGGAAGTATCGATTTAAATGATTTGAAAGAAAAAGATTTTTCCCTATCATTACAACAAAAAGGTGTTGATATGAAAATAGGTTTAGACATAGCTTCATTATCATTTAAACATCAAGTAGATAAAATTATTTTAATAGCTGGT  >  BX571857/425564‑425755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑