Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913580,4310TA56.9% 56.3 / 79.1 51I125I (ATT→ATA) ‡nohDDLP12 prophage; DNA packaging protein
Reads supporting (aligned to +/- strand):  ref base T (12/10);  new base A (12/17);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 4.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGT  >  NC_000913/580331‑580499
                                                                                                    |                                                                    
cgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAAtt                                                                      <  1:1878107/101‑1 (MQ=32)
cgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAAtt                                                                      <  2:5580080/101‑1 (MQ=32)
cgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAAtt                                                                      >  2:467825/1‑101 (MQ=32)
cgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAAtt                                                                      <  1:2750365/101‑1 (MQ=32)
 gcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTg                                                                     <  1:5895965/101‑1 (MQ=32)
 gcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTg                                                                     <  2:454966/101‑1 (MQ=32)
 gcAGGCCGATGCACAGGAGCTGAAAAATGCCAAAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATAGAAGTTGAAAGTg                                                                     >  1:407251/1‑101 (MQ=11)
  cAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGc                                                                    <  1:5474914/101‑1 (MQ=32)
   aGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGcc                                                                   <  2:2489904/101‑1 (MQ=32)
   aGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGcc                                                                   >  2:3756271/1‑101 (MQ=32)
   aGGCCGATGCACAGGAGCTGAAAAATGCCACAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGcc                                                                   >  1:6960285/1‑101 (MQ=17)
   aGGCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAATCCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGcc                                                                   <  1:3320693/101‑1 (MQ=2)
   aGGCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGcc                                                                   >  1:2681451/1‑101 (MQ=2)
   aGGCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGcc                                                                   >  1:2477984/1‑101 (MQ=2)
   aGGCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGcc                                                                   >  1:4355982/1‑101 (MQ=2)
   aGGCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGcc                                                                   <  1:1710611/101‑1 (MQ=2)
    ggCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCa                                                                  >  2:3802948/1‑101 (MQ=32)
    ggCAGATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCa                                                                  <  2:3626619/101‑1 (MQ=2)
     gcagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGTATGGCCGGAGAAGTAGCCAg                                                                 <  1:1975551/98‑1 (MQ=2)
     gcagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCac                                                                 <  2:6556548/98‑2 (MQ=2)
     gCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAg                                                                 <  2:5883146/101‑1 (MQ=32)
      ccGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGt                                                                <  1:516245/101‑1 (MQ=32)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                <  2:4072695/99‑2 (MQ=2)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                <  2:6597589/99‑2 (MQ=2)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                <  1:1447965/99‑2 (MQ=2)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                >  1:1950831/3‑100 (MQ=2)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                >  1:4341386/3‑100 (MQ=2)
      cagATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgc                                                                <  1:2645923/99‑2 (MQ=2)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAgaa                                                               >  2:428820/1‑99 (MQ=17)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  1:7024444/1‑101 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  2:1190126/1‑101 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               <  2:5623924/101‑1 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  2:2376839/1‑101 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  2:1802297/1‑101 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  2:2111446/1‑101 (MQ=32)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGGGAAATTGCCAGTa                                                               >  2:1946235/1‑101 (MQ=17)
       cGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGGGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTa                                                               >  2:511763/1‑101 (MQ=17)
       agATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAgca                                                               >  2:3774749/2‑99 (MQ=2)
        gATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCAt                                                              >  1:5428262/1‑101 (MQ=2)
        gATGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCAt                                                              >  1:6247359/1‑101 (MQ=2)
        gATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGGCGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCCGGCGAAATGGCCAGCAt                                                              >  2:1534222/1‑101 (MQ=11)
        gATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTAt                                                              <  1:3644202/101‑1 (MQ=32)
        gATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTAt                                                              >  1:864220/1‑101 (MQ=32)
        gATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATAGCCAGTan                                                              >  2:5992209/1‑100 (MQ=17)
         aTGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCAtt                                                             >  2:1974867/1‑101 (MQ=2)
         aTGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTAtt                                                             >  1:2927920/1‑101 (MQ=31)
         aTGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTAtt                                                             <  2:305349/101‑1 (MQ=31)
          tGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtc                                                            <  2:4213288/101‑1 (MQ=2)
          tGCCCAGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtc                                                            <  1:2078736/101‑1 (MQ=2)
           gcccaGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtct                                                           <  2:3107851/98‑1 (MQ=0)
           gcccaGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtct                                                           <  2:1906516/98‑1 (MQ=0)
           gcccaGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtct                                                           >  2:1300298/4‑101 (MQ=0)
           gcccaGGAACTAAAAAATGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATtcg                                                           <  2:1013141/98‑2 (MQ=0)
            caaaGGAGCTGAAAAATACCAGAGACTCCGCAGAAGTGGTGGAAACCGCATTCGGCACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATtctc                                                          <  2:1797633/98‑1 (MQ=1)
                                                                   cacgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAta   <  1:4403845/97‑2 (MQ=0)
                                                                   cacgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAta   >  2:1666857/5‑100 (MQ=0)
                                                                   cacgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAta   >  1:759642/5‑100 (MQ=0)
                                                                   cacgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAta   <  1:1066459/97‑2 (MQ=0)
                                                                    acgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAtat  <  1:381864/98‑3 (MQ=0)
                                                                    acgttCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACAtat  <  1:2896290/98‑3 (MQ=0)
                                                                                                    |                                                                    
CGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGT  >  NC_000913/580331‑580499

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑