Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,553,0310CT21.3% 96.9 / 17.8 47A227V (GCA→GTA) amiAN‑acetylmuramoyl‑l‑alanine amidase I
Reads supporting (aligned to +/- strand):  ref base C (19/18);  new base T (5/5);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACAGATACCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACGGCTGTTAGGCACGGCGG  >  NC_000913/2552932‑2553126
                                                                                                   |                                                                                               
aaaCAGATACCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGc                                                                                                 <  1:1059015/100‑1 (MQ=255)
aaaCAGATACCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGc                                                                                                 <  2:773698/100‑1 (MQ=255)
       tACCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTtgtg                                                                                          <  2:1151434/100‑1 (MQ=255)
        aCCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTgtgg                                                                                         <  2:382676/100‑1 (MQ=255)
          cATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTgtggtg                                                                                       <  2:1085710/100‑1 (MQ=255)
          cATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTgtggtg                                                                                       >  2:387224/1‑100 (MQ=255)
           aTTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGgtgt                                                                                      >  1:354219/1‑100 (MQ=255)
           aTTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGgtgt                                                                                      >  2:306173/1‑100 (MQ=255)
           aTTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAACTTAAGCCGGTGCATAAACTGCACAGCCGAAACACCGAACAAGCGGCATATgtggt                                                                                        >  2:208543/1‑98 (MQ=255)
             tAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTg                                                                                    <  2:1267583/100‑1 (MQ=255)
              aaaaaTAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTg                                                                                    >  1:655896/1‑99 (MQ=255)
                    aGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCAc                                                                             <  2:372089/100‑1 (MQ=255)
                     gTCTGACGCTCTGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACGCCGAACAAGCGGTATTTGTGGTGTTGAAATCAcc                                                                            >  2:687377/1‑100 (MQ=255)
                     gTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCAcc                                                                            >  1:809383/1‑100 (MQ=255)
                             ctcggctcgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTc                                                                    >  2:1052902/1‑100 (MQ=255)
                               cggctcgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTACACAGCCGCAACACCGAACACGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCt                                                                  >  2:1286214/1‑100 (MQ=255)
                                ggctcgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCtt                                                                 >  1:1149267/1‑100 (MQ=255)
                                  ctcgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCg                                                               >  2:948428/1‑100 (MQ=255)
                                   tcgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCgg                                                              <  2:418821/100‑1 (MQ=255)
                                    cgCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGt                                                             >  2:761962/1‑100 (MQ=255)
                                      cATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGc                                                           <  1:208580/100‑1 (MQ=255)
                                      cATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGc                                                           <  1:208200/100‑1 (MQ=255)
                                       atatTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCt                                                          >  2:1240157/1‑100 (MQ=255)
                                          ttCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCtggt                                                       >  1:839262/1‑100 (MQ=255)
                                           tCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCtggt                                                       >  1:909367/1‑99 (MQ=255)
                                            cTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCtggtgg                                                     <  2:922719/100‑1 (MQ=255)
                                             tGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGa                                                    <  2:9895/100‑1 (MQ=255)
                                               aagaagATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGaaa                                                  >  1:1066107/1‑100 (MQ=255)
                                                agaagaTTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAAc                                                 >  1:492686/1‑100 (MQ=255)
                                                 gaagaTTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAAcc                                                >  1:323324/1‑100 (MQ=255)
                                                      ttAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGtt                                           <  2:471231/100‑1 (MQ=255)
                                                      ttAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGtt                                           <  2:349689/100‑1 (MQ=255)
                                                      ttAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGtt                                           <  2:613143/100‑1 (MQ=255)
                                                        aaGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTa                                         <  2:354216/100‑1 (MQ=255)
                                                         aGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTAt                                        >  1:688545/1‑100 (MQ=255)
                                                          gCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATc                                       >  2:774204/1‑100 (MQ=255)
                                                          gCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATc                                       <  1:306176/100‑1 (MQ=255)
                                                               tGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCaa                                  <  1:735293/100‑1 (MQ=255)
                                                                gCATAAACTGCACAGCCGCAACACCGAACAAGCGGTATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAAc                                 >  1:108270/1‑100 (MQ=255)
                                                                 cATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAAcc                                >  2:399908/1‑100 (MQ=255)
                                                                 cATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAAcc                                <  1:576911/100‑1 (MQ=255)
                                                                  aTAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAAccc                               >  2:836439/1‑100 (MQ=255)
                                                                    aaaCTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCgg                             <  2:1233663/100‑1 (MQ=255)
                                                                       cTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGgaag                          <  1:562349/100‑1 (MQ=255)
                                                                              gCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACg                   <  1:195282/100‑1 (MQ=255)
                                                                              gCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACg                   <  1:729871/100‑1 (MQ=255)
                                                                                            cAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACGGCTGTTAGGCAcgg     <  1:497584/100‑1 (MQ=255)
                                                                                              aGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACGGCTGTTAGGCAcggcg   <  1:399912/100‑1 (MQ=255)
                                                                                               gCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACGGCTGTTAGGCAcggcgg  >  1:1232433/1‑100 (MQ=255)
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AAACAGATACCATTAAAAATAGTCTGACGCTCGGCTCGCATATTCTGAAGAAGATTAAGCCGGTGCATAAACTGCACAGCCGCAACACCGAACAAGCGGCATTTGTGGTGTTGAAATCACCGTCGGTTCCTTCGGTGCTGGTGGAAACCTCGTTTATCACCAACCCGGAAGAAGAACGGCTGTTAGGCACGGCGG  >  NC_000913/2552932‑2553126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑