Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 289,257 T→A 9.0% intergenic (‑95/+44) yagI ← / ← argF CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913289,2570TA 9.0% 100.8 / 2.9 45intergenic (‑95/+44)yagI/argFCP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
Reads supporting (aligned to +/- strand):  ref base T (28/11);  new base A (2/2);  total (30/15)
Fisher's exact test for biased strand distribution p-value = 5.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-01

GTTGAACAGGTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCA  >  NC_000913/289109‑289404
                                                                                                                                                    |                                                                                                                                                   
gTTGAACAGGTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCtgt                                                                                                                                                     >  1:620545/1‑149 (MQ=255)
      cAGGTCGAGGATCTGCAACGCCCGTTCAACAGACTGAATAATCGGCATAATGCGGGCATGTCCACGATGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCACTGAAATCGAGCCGGTGTTCTCCCTCTCCCTGTGGgaga                                                                                                                                               >  2:871443/1‑149 (MQ=255)
      cAGGTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGgaga                                                                                                                                               <  1:412373/149‑1 (MQ=255)
       aGGTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCACAGGGagag                                                                                                                                              <  1:620276/149‑1 (MQ=255)
         gTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGATTTAAGGCGAAACAGTACCTATTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCACGCCCTGTGGGAGAggg                                                                                                                                            >  2:1049607/1‑149 (MQ=255)
          tCGAGGATCTGCAACGCACGTTCACCAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTCTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGc                                                                                                                                           >  2:1083031/1‑149 (MQ=255)
          tCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGTATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCACAGGGAGAggga                                                                                                                                           <  2:664751/149‑2 (MQ=255)
            gAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCg                                                                                                                                         >  2:493381/1‑149 (MQ=255)
              ggATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCggg                                                                                                                                       <  2:106608/149‑1 (MQ=255)
              ggATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCggg                                                                                                                                       <  1:418214/149‑1 (MQ=255)
                   tGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAg                                                                                                                                  >  2:1164947/1‑149 (MQ=255)
                   tGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCAGGTCCACGCTGCAATTAAGGCGAAAACGTACCTTTTTCGGGAGGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAg                                                                                                                                  <  2:650284/149‑1 (MQ=255)
                   tGCAACGCACGTTCAACAGACTGAAAAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCACTGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAg                                                                                                                                  >  2:49444/1‑149 (MQ=255)
                       acccACGTGCAACAGACTGACTAAGCGGCATAATGCTGGCAAGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCa                                                                                                                              <  2:1116088/146‑1 (MQ=39)
                             gTTCAACAGACTGAATAATCGGCATAATGCTGGCAAGTCCCCGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAAcg                                                                                                                        >  1:964290/1‑149 (MQ=255)
                              ttCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAAcgc                                                                                                                       >  2:507867/1‑149 (MQ=255)
                                   cAGACTGAATATTCGGCATAATGCTGGCATGACCAGGCTCGAATTAAGGCGAAACCGTCCCTTTTTCGGTATGAAAAATCAATCAAATGGCGCCGTTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGTGGGCACCAACGCGCAGc                                                                                                                  <  2:757785/149‑1 (MQ=37)
                                      aCTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCggc                                                                                                               >  2:40727/1‑148 (MQ=255)
                                          aataatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGAcccc                                                                                                           >  1:821421/1‑148 (MQ=255)
                                            taatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTAGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGTGAGAGGGCCGGGGTGAGGGCACCAACGCGCATCGGACCCaaa                                                                                                         >  1:905878/1‑148 (MQ=255)
                                             aatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTCCCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATc                                                                                                        >  2:1046980/1‑149 (MQ=255)
                                                    aTAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTcccc                                                                                                 >  2:858315/1‑149 (MQ=255)
                                                          cTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCACCGCGCAGCGGACCCAATCACTCCCCAAGCGt                                                                                           >  1:672076/1‑149 (MQ=255)
                                                               aTGTCCACGCTGTAATTACGGCCAAACCGTACCTTTTGCGGTATTAAAACACAATCAAAGGGCGCCGGGGTACTCCCTCTCCCTGGGGGCGAGGGCCGGGGGGCGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCca                                                                                      <  2:685926/149‑1 (MQ=255)
                                                                   ccACGCTGTAATTACGCCTAAACCGTCCATTTTTCGGTATTAAAAATCAATCAATTGGCGCGGGGGTTCCCCCTCTCCCTGTGGTTGTGGGCGGGGGTGCGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatcat                                                                                  <  1:25952/149‑1 (MQ=255)
                                                                              ttAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCACCATCACCGCCTTaa                                                                       >  1:55304/1‑149 (MQ=255)
                                                                                  ggCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCACTCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGt                                                                   >  2:587906/1‑149 (MQ=255)
                                                                                  ggCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCCCTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGt                                                                   >  1:310917/1‑149 (MQ=255)
                                                                                  ggCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGt                                                                   >  1:307609/1‑149 (MQ=255)
                                                                                         ccGTTCCTTTTTCGGGATGAAAAATCAATGAAATGGTGCCGGTGTTCGCCCTCTCCCGGTGGGAGAGGGCCGGGTGGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATc                                                            <  2:639991/148‑1 (MQ=255)
                                                                                                 ttttCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGTAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGCTGCCATCATCACCGCCTTAATCGTAGGCATCCGGTTTTc                                                    >  1:197135/1‑149 (MQ=255)
                                                                                                      gggATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCCACGCGCAGCGGACCCAATCAGTCCCCAAGCGTTGCCATCATGCCCGCGTTAATCGTATGCTTCCGGTTTTCCGCCt                                               >  2:1179781/1‑149 (MQ=38)
                                                                                                       gtattaaaaaTCAATTAATGGCCGCGGGTGTGCGCCCTCGCCCTGTGGGTGTGGGCGGGGGTGCGGCCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTg                                              <  2:488374/144‑1 (MQ=255)
                                                                                                       gtaaaaaaaaCCAATAACTTGGCGCGGGTGTGCCCCCTCCCCCTGGGGGTGTGGGGGGGGGGGCGGCCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTg                                              <  2:620545/144‑1 (MQ=255)
                                                                                                        gATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCACGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTgg                                             >  2:177589/1‑149 (MQ=255)
                                                                                                           gAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCg                                          >  1:1174591/1‑149 (MQ=255)
                                                                                                           gAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGGTTTCGGCCTGGTCg                                          >  1:490518/1‑149 (MQ=255)
                                                                                                            aaaaaTCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCACTCACTCCCCAAGCGTTGCCCTCATCACCGCCTTAATCGTATGCCTCCGGTTTTCCGCCTGGTCgc                                         >  1:87706/1‑148 (MQ=255)
                                                                                                            aaaaaTCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGCGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCACCAAACGTTGCCCTCATCACCGCCATAATCGTATGCATCCGGTAAACCGCCTGGTCGa                                         >  1:209078/1‑149 (MQ=38)
                                                                                                                     tGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGc                                >  1:102555/1‑149 (MQ=255)
                                                                                                                                      tctccctctcccTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAac               >  2:458473/1‑149 (MQ=255)
                                                                                                                                      cggccctctcccaCAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCCAGCGTTGGCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGCCTCAAac               >  2:49399/4‑149 (MQ=255)
                                                                                                                                      cggccctctcccaCAGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCCAGCGGTGCCCTCATCACCGCCTTAATAGTATGCATCCGGGTTTCCGCCTGGTCGACCCCGATGCTCGCCGCCCGCTCAAac               >  1:285779/4‑149 (MQ=255)
                                                                                                                                       ctccctctccctGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAaca              >  2:488090/1‑149 (MQ=255)
                                                                                                                                         ccctctccctGTTGCTTTGGGCCGGGGGTTGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACAcc            <  1:223742/149‑1 (MQ=255)
                                                                                                                                         cacgatccctGTGGAATCGGGCGGGGGGGTGCCCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACAcc            <  1:656466/144‑1 (MQ=255)
                                                                                                                                                   gtgGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTACCCAAGCGTTGCCATCATCACCGCCTTAATCGTATTCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGACGCCGACTCAAACACCTCGTCCGTCa  >  2:740956/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
GTTGAACAGGTCGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTCGGGATGAAAAATCAATGAAATGGAGCCGGTGTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCA  >  NC_000913/289109‑289404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑