Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,035,886 T→C 66.2% intergenic (‑212/‑3) USA300HOU_1892 ← / → USA300HOU_1893 hypothetical protein/DNA‑directed DNA polymerase III

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,035,8860TC66.2% 21.7 / 12.5 24intergenic (‑212/‑3)USA300HOU_1892/USA300HOU_1893hypothetical protein/DNA‑directed DNA polymerase III
Reads supporting (aligned to +/- strand):  ref base T (3/5);  new base C (12/3);  total (16/8)
Fisher's exact test for biased strand distribution p-value = 7.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAA  >  CP000730/2035746‑2036023
                                                                                                                                            |                                                                                                                                         
tcatcaTTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAACGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGCTTTACt                                                                                                                                           >  2:82591/1‑141 (MQ=255)
     atTTACTTTTTAATCAGAGTTACATCCAAATGATGGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTATAAGCAAATGACTAAAAGTATATTAATATATACATTTAATTAATTGCAAGGATTTACCACATg                                                                                                                                      >  2:84314/1‑141 (MQ=255)
          cTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTAAAATGATTGACAACATGATACa                                                                                                                                 >  1:84095/1‑141 (MQ=255)
                                        gATTTCACGTTATACCATCACGTATAATACTATGACTCGAGTGATAGCAAATGACTAAGAGTCTATTAATATATACATTTAACTAATTGAAAGGATTGTCTACCTGATACAAGATGCGTTTGTGGCACTTGATATTGAGAc                                                                                                   >  2:127866/1‑141 (MQ=255)
                                             aaatatataCCTTGAATAATAATATGATGTATGGTTTGTAAGGATATGTCTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTAAATGATACAAGATGCGTTTGTTGCACTAGATTTTGAAACAGCaa                                                                                              <  1:51274/136‑1 (MQ=255)
                                                            cGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               <  2:159855/141‑1 (MQ=255)
                                                             gTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACTAGACGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAg                                                                              <  1:192438/141‑1 (MQ=255)
                                                                  atatTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTAttt                                                                         >  2:254382/1‑141 (MQ=255)
                                                                             cGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCATTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGa                                                              <  2:206353/141‑1 (MQ=255)
                                                                                   tAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGtt                                                        >  1:44740/1‑141 (MQ=255)
                                                                                   tAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGtt                                                        >  1:233780/1‑141 (MQ=255)
                                                                                         aaTGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTTTCGGAATGGATAAAGTc                                                  >  2:191992/1‑141 (MQ=255)
                                                                                            gACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCAtt                                               >  1:225149/1‑141 (MQ=255)
                                                                                              cTAAAAGTCTATTACTATATACATTTCATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACCGCTAATGTTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGa                                             <  1:162539/141‑1 (MQ=255)
                                                                                                       tATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAAt                                    >  1:275861/1‑141 (MQ=255)
                                                                                                        aTTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAAGGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATa                                   >  2:120003/1‑141 (MQ=255)
                                                                                                                ataCATTTAATTAATTGAAAGGATTGACCACATGATACAAGATACGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGACTGGCTACAGTCAATGATAGTACAATAACAGaaaa                           >  1:26839/1‑140 (MQ=255)
                                                                                                                     tttAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCACATGGTAAACGTACAAGTATTTGTCCTGTCGGAATGGTTAAAGTCATTGTTAGTCAAATAACAAAACCAGTTc                      >  2:41759/1‑141 (MQ=255)
                                                                                                                     tttAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTc                      <  1:254382/141‑1 (MQ=255)
                                                                                                                         attaattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               <  1:77535/80‑1 (MQ=255)
                                                                                                                         attaattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               >  2:77535/1‑80 (MQ=255)
                                                                                                                              ttGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTtg             <  1:117921/141‑1 (MQ=255)
                                                                                                                                        tGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCa   >  1:191751/1‑141 (MQ=255)
                                                                                                                                         gACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCaa  >  1:257778/1‑141 (MQ=255)
                                                                                                                                         gACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAACCCGCaa  >  2:76687/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                         
TCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAA  >  CP000730/2035746‑2036023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: