Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 564,435 C→G 7.6% C256S (TGT→TCT)  intD ← predicted integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb564,4350CG 7.6% 220.7 / 5.5 79C256S (TGT→TCT) intDpredicted integrase
Reads supporting (aligned to +/- strand):  ref base C (38/34);  new base G (4/2);  total (42/37)
Fisher's exact test for biased strand distribution p-value = 6.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GCTTAGCCGCCTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCAGGC  >  W3110S.gb/564367‑564502
                                                                    |                                                                   
gCTTAGCCGCCTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAg                                                                   >  1:2828050/1‑71 (MQ=255)
  ttAGCCGCCTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGc                                                                 >  1:2636086/1‑71 (MQ=255)
    aGCCGCCTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAgg                                                                  <  1:2148513/68‑1 (MQ=255)
        gccCTGGTATGTAC‑‑ACCCACATTTGTGATGCTTGCCTGTTTGATCATGCAGCACTTTAGAGGCGGTATCGt                                                         >  1:3214244/1‑71 (MQ=255)
         ccTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCg                                                          <  1:3688050/71‑1 (MQ=255)
           ttGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        >  1:2813291/1‑71 (MQ=255)
            tGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        >  1:4246039/1‑70 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:2823030/69‑1 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:89965/69‑1 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:1814966/69‑1 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:2530412/69‑1 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:2514899/69‑1 (MQ=255)
             ggTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        <  1:1134646/69‑1 (MQ=255)
               tATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAgc                                                    <  1:3557143/71‑1 (MQ=255)
               tATGTACAAACACCCATTTGTGATGCTTGACTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAgc                                                    <  1:4406546/71‑1 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGGAACACTTTACAGGCGGTATCg                                                          <  1:3502997/61‑1 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACa                                                                    >  1:4197465/1‑51 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:3339764/1‑71 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:3080135/1‑71 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:2559292/1‑71 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:1070787/1‑71 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:4383577/1‑71 (MQ=255)
                   tACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGG‑GGTATCGTTCAGCGCca                                                >  1:600477/1‑70 (MQ=255)
                    aCAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACa                                                                    >  1:95722/1‑50 (MQ=255)
                    aCAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTc                                                       >  1:1801326/1‑63 (MQ=255)
                     cAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACa                                                                    >  1:3528257/1‑49 (MQ=255)
                       aaCACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACAcc                                            <  1:1653331/71‑1 (MQ=255)
                        acacCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACAcc                                            >  1:3294236/1‑70 (MQ=255)
                        acacCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACAcc                                            >  1:3618639/1‑70 (MQ=255)
                         cacCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTTCAGGCGGTATCGt                                                         <  1:2620947/56‑1 (MQ=255)
                          acCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACAcc                                            <  1:1812351/68‑1 (MQ=255)
                          acCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAAt                                         <  1:914194/71‑1 (MQ=255)
                          acCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAAt                                         <  1:2918340/71‑1 (MQ=255)
                           cccATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGtt                                                        >  1:4372473/1‑55 (MQ=255)
                            ccATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTAc                                                                     >  1:1428608/1‑41 (MQ=255)
                            ccATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATgg                                       >  1:1981901/1‑71 (MQ=255)
                              aTTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAgcgc                                                  >  1:3104029/1‑58 (MQ=255)
                               tttGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGc                                                                 <  1:4204927/42‑1 (MQ=255)
                                 tgtgATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:4283160/1‑57 (MQ=255)
                                 tgtgATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCca                                                >  1:790685/1‑57 (MQ=255)
                                 tgtgATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCaa                                          >  1:1594150/1‑63 (MQ=255)
                                 tgtgATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCgg                                  >  1:2726701/1‑71 (MQ=255)
                                  gtgATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCgg                                  <  1:2897340/70‑1 (MQ=255)
                                   tgATGCTTGCCTGTTTGATCATGCAGCACTTTAGAGGCGGTATCGTTCAGCGCCACACCAATGGcgcga                                  <  1:3097259/69‑2 (MQ=255)
                                   tgATGCTTGCCTGTTTGATCATGCAGCACTTTAGAGGCGGTATCGTTCAGCGCCACACCAATGGcgcga                                  <  1:2712861/69‑2 (MQ=255)
                                     aTGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGttt                               <  1:4329439/70‑1 (MQ=255)
                                     aTGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTg                              <  1:4238773/71‑1 (MQ=255)
                                     aTGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTg                              <  1:108242/71‑1 (MQ=255)
                                     aTGCTTGCCTATTTGATCACGCAACACTTTAAAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTg                              <  1:3372523/71‑1 (MQ=255)
                                        cTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGAt                            <  1:3847525/70‑1 (MQ=255)
                                           gCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTg                         <  1:3015047/70‑1 (MQ=255)
                                           gCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTg                         <  1:3012190/70‑1 (MQ=255)
                                           gCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACA‑CAATGGCGCGGTTTGATTTg                         <  1:3385063/69‑1 (MQ=255)
                                             caaTTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGctc                      >  1:3300997/3‑71 (MQ=255)
                                             cTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTCTGATTTGctc                      <  1:1898787/71‑1 (MQ=255)
                                              tATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCgg                                  <  1:496594/58‑1 (MQ=255)
                                               aTTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGctctc                    >  1:411666/1‑71 (MQ=255)
                                                tttGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATgg                                       >  1:2415193/1‑51 (MQ=255)
                                                tttGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGctctc                    <  1:4096374/70‑1 (MQ=255)
                                                tttGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGctctc                    <  1:669076/70‑1 (MQ=255)
                                                 ttGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGct                       >  1:1737837/1‑66 (MQ=255)
                                                 ttGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGct                       >  1:2671364/1‑66 (MQ=255)
                                                  tGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCtcttc                 >  1:1286843/1‑71 (MQ=255)
                                                   gATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCtcttc                 <  1:3642529/70‑1 (MQ=255)
                                                    aTCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCtcttct                <  1:3071825/70‑1 (MQ=255)
                                                      catgcagcaCTTTAGAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGATTTGATTTGctatc                    >  1:3738736/4‑64 (MQ=255)
                                                      catgcagcaCTTTAGAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGATTTGATTTGctatc                    >  1:2806545/4‑64 (MQ=255)
                                                      catgcagcaCTTTAGAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGATTTGATTTGctatc                    >  1:3394933/4‑64 (MQ=255)
                                                      cACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGAtt                           >  1:2674254/1‑57 (MQ=255)
                                                      cACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGa             >  1:1286544/1‑71 (MQ=255)
                                                       aCGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGa             <  1:1488191/70‑1 (MQ=255)
                                                         gCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCgg                                  >  1:1592740/1‑47 (MQ=255)
                                                             cacTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGttt                               <  1:3800973/46‑1 (MQ=255)
                                                             cacTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCAcc       >  1:2796007/1‑70 (MQ=255)
                                                              acTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCAcc       >  1:2103666/1‑69 (MQ=255)
                                                               cTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGa                             >  1:1910002/1‑46 (MQ=255)
                                                               cTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCa     >  1:2673393/1‑70 (MQ=255)
                                                                 ttACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCAgg   >  1:2618395/1‑70 (MQ=255)
                                                                  tACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCAGGc  <  1:2318069/70‑1 (MQ=255)
                                                                  tACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCAGGc  >  1:1176539/1‑70 (MQ=255)
                                                                    |                                                                   
GCTTAGCCGCCTTGGTATGTACAAACACCCATTTGTGATGCTTGCCTATTTGATCACGCAACACTTTACAGGCGGTATCGTTCAGCGCCACACCAATGGCGCGGTTTGATTTGCTCTCTTCTGGATTCACCCAGGC  >  W3110S.gb/564367‑564502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑