Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,634,9580GC24.4% 100.4 / 27.7 41T297S (ACC→AGC) stfQQin prophage; putative side tail fibre assembly protein
Reads supporting (aligned to +/- strand):  ref base G (16/15);  new base C (0/10);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 3.18e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.68e-01

TCATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGG  >  NC_000913/1634870‑1635054
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tCATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacg                                                                                       <  1:57461/100‑5 (MQ=1)
tCATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacg                                                                                       <  2:1147152/100‑5 (MQ=1)
 cATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgc                                                                                      <  2:1529580/100‑6 (MQ=1)
 cATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgc                                                                                      <  2:2250310/100‑6 (MQ=1)
  aTTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcg                                                                                     <  2:1441534/100‑7 (MQ=1)
  aTTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcg                                                                                     <  2:1166819/100‑7 (MQ=1)
   ttCTGGATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcgg                                                                                    <  2:2366703/100‑8 (MQ=1)
   ttCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcgg                                                                                    <  1:2186886/100‑8 (MQ=1)
   ttCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcgg                                                                                    <  2:2776639/100‑8 (MQ=1)
   ttCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCATCACCGTTAACGCTGCTGgtaacgcgg                                                                                    <  1:1870240/100‑8 (MQ=1)
                 atacAAGCCTCACAATATAGTTAAATGCGATGTTGTTGACGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGc                                                                      <  2:311471/97‑1 (MQ=0)
                                                       aCGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTAtgtg                                >  2:2651193/1‑100 (MQ=31)
                                                       aCGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTAtgtg                                <  2:22667/100‑1 (MQ=31)
                                                        cGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGc                               >  2:2152380/1‑100 (MQ=32)
                                                         ggTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGcn                              <  1:2494025/100‑2 (MQ=17)
                                                         ggTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCa                              >  2:455256/1‑100 (MQ=33)
                                                          gtgtTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCAt                             >  1:1137454/1‑100 (MQ=35)
                                                            gtTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATgc                           >  1:1559450/1‑100 (MQ=38)
                                                                   gcgTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTg                    <  1:2325501/100‑1 (MQ=255)
                                                                   gcgTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTg                    <  1:2189479/100‑1 (MQ=255)
                                                                    cgTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTgc                   >  2:2319434/1‑100 (MQ=255)
                                                                    cgTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTgc                   >  2:2319354/1‑100 (MQ=255)
                                                                    cgTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTgc                   <  2:2474753/100‑1 (MQ=255)
                                                                     gTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTgcg                  >  1:429621/1‑100 (MQ=255)
                                                                       tACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCt                <  1:1727601/100‑1 (MQ=255)
                                                                       tACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCt                <  2:2210975/100‑1 (MQ=255)
                                                                        aCCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCtt               >  2:1008547/1‑100 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             <  1:1148347/100‑1 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             >  2:1230976/1‑100 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             >  1:936254/1‑100 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             <  1:2646324/100‑1 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             >  1:2370730/1‑100 (MQ=255)
                                                                          cagcagCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgc             >  1:2370716/1‑100 (MQ=255)
                                                                             cagcGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTgcacatactgt          <  1:273472/100‑10 (MQ=255)
                                                                              agcGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTgcagca         >  2:2232038/1‑100 (MQ=255)
                                                                               gcGTAAACGGGGATGGTGTGTCCATGTGAACCAACCGCAACGGAGTGCGTAGGAGCACCAATACCGACAGTATTTGCATGCGCGCCTGCGCTTGcagcag        <  2:1462676/100‑1 (MQ=14)
                                                                                cGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGt       >  1:1934385/1‑100 (MQ=255)
                                                                                 cttAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTg      <  2:57489/99‑1 (MQ=255)
                                                                                   tAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTgag    >  1:57492/1‑98 (MQ=255)
                                                                                    aaCGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCg   <  1:613625/100‑1 (MQ=255)
                                                                                     aCGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCgg  <  1:869876/100‑1 (MQ=255)
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TCATTCTGAATGCCATTATGCAAGCCTCACAATATAGTTAAATGCGATGTTTTTGACGGTGTTTTCCGCGTTACCAGCAGCGTTAACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGG  >  NC_000913/1634870‑1635054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: