Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,413,092 C→T A48A (GCG→GCA)  intR ← putative integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,413,0920CT96.0% 80.0 / ‑6.3 25A48A (GCG→GCA) intRputative integrase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (16/8);  total (17/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

ATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTG  >  NC_000913/1412868‑1413330
                                                                                                                                                                                                                                |                                                                                                                                                                                                                                              
atCGGGGTACTTTCACAAATTATTATTCTGAGAGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTACATCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCCCCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAat                                                                                                                                                                                                                      >  2:146033/1‑251 (MQ=255)
    gggTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGACTTTTTAATAtt                                                                                                                                                                                                                   >  1:406618/1‑250 (MQ=255)
            tCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTa                                                                                                                                                                                                                                         >  2:262848/1‑220 (MQ=255)
            tCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTa                                                                                                                                                                                                                                         <  1:262848/220‑1 (MQ=255)
              acaAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTa                                                                                                                                                                                                         >  1:102779/1‑250 (MQ=255)
                                              aTTTCGTTTTCTTCCTTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTTGGGACAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGt                                                                                                                                                                        >  2:368196/1‑251 (MQ=255)
                                                         ttcATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGaa                                                                                                                                                              >  1:111952/1‑250 (MQ=255)
                                                                  tttgttGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTAACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGCACTATCAGTGCTCTTAAATTTCCGGACTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGacccc                                                                                                                                                    >  2:437941/1‑247 (MQ=255)
                                                                            aCTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATg                                                                                                                                          >  1:69801/1‑251 (MQ=255)
                                                                              tctGTCTCTTTAATTTTTGTCAAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGTTGCGAATGt                                                                                                                                         >  1:374410/1‑250 (MQ=255)
                                                                               ctGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGt                                                                                                                                         <  1:208039/249‑1 (MQ=255)
                                                                                               tGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCg                                                                                                                        <  1:131795/250‑1 (MQ=255)
                                                                                                gTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGac                                                                                                                      <  1:53625/251‑1 (MQ=255)
                                                                                                gTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGac                                                                                                                      >  1:114681/1‑251 (MQ=255)
                                                                                                                   ctcCGACCGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGAc                                                                                                   >  2:189714/1‑251 (MQ=255)
                                                                                                                           gTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCCGTGCTGGACTGGGGAAAACGTCTTACATACTCAAATTCACCGGAGTTTATTTCATGAACTCTCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGCAATTTAGACATCTCATg                                                                                           >  2:450413/1‑251 (MQ=255)
                                                                                                                                tATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCt                                                                                      >  2:262876/1‑251 (MQ=255)
                                                                                                                                   gACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTg                                                                                   <  1:180892/251‑1 (MQ=255)
                                                                                                                                                 ccattgtggCCCCAGTGCTGCACTGGGGAAAACGTCTTAAATACTCAAATTCACCGTAGTTTATTTCATTAACTATTAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCTTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGTCACCTGTTTGTAATTTTGACATATCATGAGTCTTTGATAAACTGATTTAt                                                                     <  2:17488/243‑1 (MQ=255)
                                                                                                                                                  cATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATc                                                                    >  2:261486/1‑251 (MQ=255)
                                                                                                                                                                                    cTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCCTGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGCTAATCCCTCGTTTGc                                  >  2:87166/1‑251 (MQ=255)
                                                                                                                                                                                         aTACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCt                             >  1:298239/1‑251 (MQ=255)
                                                                                                                                                                                                           gTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGTATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAgg               >  2:10263/1‑247 (MQ=255)
                                                                                                                                                                                                                 ttCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCg      <  2:298239/250‑1 (MQ=255)
                                                                                                                                                                                                                    aTGAACTATAAGTGCTCGTAAATTGTCGGCCTTTTTAATATTACTGTGTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCACGAAACGTGAACCAGATGCGAATGTATCTACCTCTAATCTCGACTCCTGTTGGTAATTTAGACATATCATGAGTCTGTGATAAACTGATTTATCTTTTGATAGTTGTACCAGATAATCCCTCGTTTGCTTTCTGTCTTACCTAAAGGAGATACTCGTTTg  <  2:198597/251‑1 (MQ=255)
                                                                                                                                                                                                                                |                                                                                                                                                                                                                                              
ATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTG  >  NC_000913/1412868‑1413330

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑