Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 790,778 G→A 100% intergenic (+277/‑197) USA300HOU_0741 → / → USA300HOU_0742 possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730790,7780GA100.0% 126.4 / NA 39intergenic (+277/‑197)USA300HOU_0741/USA300HOU_0742possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/16);  total (23/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATG  >  CP000730/790640‑790910
                                                                                                                                          |                                                                                                                                    
tttACTTGAATTTTGACTAAAATTAATCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTtata                                                                                                                                    >  2:515737/1‑141 (MQ=255)
          ttttTACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATa                                                                                                                          <  2:116858/141‑1 (MQ=255)
                   aaaTTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTaaa                                                                                                                 >  1:205588/1‑141 (MQ=255)
                    aaTTACTCTATTTTTATTAATTTTGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAGACTTACTCAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAAt                                                                                                                <  2:280320/141‑1 (MQ=255)
                     aTTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATc                                                                                                               <  1:509392/141‑1 (MQ=255)
                      ttACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCa                                                                                                              >  2:354724/1‑141 (MQ=255)
                        aCTCTATATTTATTAATTGACCTATGCTTATTATTACAATTTGATTGCAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACGCAAGCCAATATGAGTTATAGCCCAAAAGACTTGTTAAATCaaa                                                                                                            >  1:395020/1‑141 (MQ=255)
                                  tattaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTGGAAAGCt                                                                                                  >  1:30362/1‑141 (MQ=255)
                                       aTTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTAaaaa                                                                                             >  1:229138/1‑141 (MQ=255)
                                                tGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGaaaa                                                                                    >  1:387039/1‑141 (MQ=255)
                                                     attattaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATtata                                                                               <  1:485484/141‑1 (MQ=255)
                                                        attaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAAc                                                                            <  1:484633/141‑1 (MQ=255)
                                                           ccAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCACAATACTTGTTAAATCAAAGTTGCAAGCTACAAATAACTAAAATTATAATCTTg                                                                         <  2:341627/140‑1 (MQ=255)
                                                           aCAATTTTATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTg                                                                         <  2:2651/141‑1 (MQ=255)
                                                           aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGCTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTg                                                                         <  2:12791/141‑1 (MQ=255)
                                                              aTTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAAt                                                                      >  2:522162/1‑141 (MQ=255)
                                                               tttGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATc                                                                     <  1:441219/141‑1 (MQ=255)
                                                                  gATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGa                                                                  <  2:443277/141‑1 (MQ=255)
                                                                  gATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGa                                                                  <  2:459584/141‑1 (MQ=255)
                                                                           ttttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTa                                                         >  1:469593/1‑141 (MQ=255)
                                                                             ttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACt                                                       >  2:424180/1‑141 (MQ=255)
                                                                             ttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACt                                                       >  1:330734/1‑141 (MQ=255)
                                                                                aaTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACtata                                                    >  2:166804/1‑141 (MQ=255)
                                                                                     gTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTAAAAGTAATTACTATAATTAt                                               >  2:172228/1‑141 (MQ=255)
                                                                                              aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTATTATAATTATGACAATGtt                                      >  1:369986/1‑141 (MQ=255)
                                                                                              aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATAACAATGtt                                      >  2:420597/1‑141 (MQ=255)
                                                                                               tGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTa                                     >  1:197397/1‑141 (MQ=255)
                                                                                                gATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATAATTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAAATATGACAATGTTaa                                    >  2:10534/1‑141 (MQ=255)
                                                                                                  taataTTAAATAAAGAAACTTACACAAGCAAATATGCGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTAGTATAATTATGACAATGTTAACt                                  >  1:388271/1‑141 (MQ=255)
                                                                                                  taataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACt                                  <  2:22705/141‑1 (MQ=255)
                                                                                                    atatTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACttt                                <  1:515737/141‑1 (MQ=255)
                                                                                                     tatTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                               <  1:522162/141‑1 (MQ=255)
                                                                                                      atTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTa                              >  1:474544/1‑141 (MQ=255)
                                                                                                       ttAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTaa                             >  2:549231/1‑141 (MQ=255)
                                                                                                         aaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATAATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAAc                           >  2:213216/1‑141 (MQ=255)
                                                                                                                gAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACttt                    >  2:423236/1‑140 (MQ=255)
                                                                                                                        caaaaGCAAATATGAGTTATAGCCCAAAATCCTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTAttaattaa            <  1:432875/138‑1 (MQ=255)
                                                                                                                           aaGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTa         <  1:485833/141‑1 (MQ=255)
                                                                                                                                  tatGAGTTATAGCCCGAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATg  >  1:416874/1‑141 (MQ=255)
                                                                                                                                  tatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATg  >  2:496263/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                    
TTTACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATG  >  CP000730/790640‑790910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: