Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 660,088 A→T 8.9% intergenic (+349/‑18) USA300HOU_0600 → / → USA300HOU_0601 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730660,0880AT 8.9% 131.2 / 3.3 45intergenic (+349/‑18)USA300HOU_0600/USA300HOU_0601hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (20/21);  new base T (2/2);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TGGATTAAGAGATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCGTGTACTTTTTTCCTTT  >  CP000730/659954‑660224
                                                                                                                                      |                                                                                                                                        
tGGATTAAGAGATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAAc                                                                                                                                    >  2:423030/1‑141 (MQ=255)
tGGATTAAGAGATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAAc                                                                                                                                    >  2:238591/1‑141 (MQ=255)
tGGATTAAGAGATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAAc                                                                                                                                    >  2:324318/1‑141 (MQ=255)
       agagATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTATTGAAACGGGAGTg                                                                                                                             >  2:234325/1‑141 (MQ=255)
       agagATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTATTGAAACGGGAGTg                                                                                                                             >  2:234291/1‑141 (MQ=255)
       agagATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTAGTAAAGGTACAAAAAGTATTGGGGATCATATAAAACTAATGAAAAGGGAGTg                                                                                                                             >  2:287027/1‑141 (MQ=255)
        gagaTAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTgg                                                                                                                            <  1:440900/141‑1 (MQ=255)
            tAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGAAAAAGAAAAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTaaa                                                                                                                        <  2:389116/141‑1 (MQ=255)
              aaaCTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATg                                                                                                                      >  1:55970/1‑141 (MQ=255)
                      tGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGCGGTAAATGTTGCTTTg                                                                                                              >  2:170213/1‑141 (MQ=255)
                        gATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCg                                                                                                            >  1:309683/1‑141 (MQ=255)
                             aaaaTTAAATAGAAGCTGTTTAAAAATAGCACAGAAAAAGATATAGATAGTGTTGGAACGATGGTTAGTAAAAAAAAAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTc                                                                                                       <  2:90246/138‑1 (MQ=255)
                                 ttAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCagag                                                                                                   >  1:374383/1‑141 (MQ=255)
                                  tAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGt                                                                                                  <  2:253967/141‑1 (MQ=255)
                                                ttAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATc                                                                                    >  1:414814/1‑141 (MQ=255)
                                                  aaaaaTACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCg                                                                                  <  2:154250/141‑1 (MQ=255)
                                                  aaaaaTACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCg                                                                                  >  2:102865/1‑141 (MQ=255)
                                                    aaaTACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGaa                                                                                >  1:81596/1‑141 (MQ=255)
                                                      aTACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAAt                                                                              >  2:430698/1‑141 (MQ=255)
                                                        aCCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATAc                                                                            >  2:236292/1‑141 (MQ=255)
                                                             aGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGAACATTTAAAACTAATGAAACGGGAGTGGTAAATACTGCTATGGGATGACAGAAAAATATATAAAAAGCCGAAATACAAAGt                                                                       >  1:242927/1‑141 (MQ=255)
                                                                  aaGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTc                                                                  <  1:283402/141‑1 (MQ=255)
                                                                    gCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCaa                                                                <  1:245866/141‑1 (MQ=255)
                                                                      tGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTATTGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACa                                                              <  1:234325/141‑1 (MQ=255)
                                                                      tGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTATTGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACa                                                              <  1:234291/141‑1 (MQ=255)
                                                                        tAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATa                                                            >  1:25093/1‑141 (MQ=255)
                                                                           aTAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACg                                                         <  2:344114/141‑1 (MQ=255)
                                                                             aGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGt                                                       <  1:2390/141‑1 (MQ=255)
                                                                                 ttGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAAt                                                   <  2:55970/141‑1 (MQ=255)
                                                                                  tGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATa                                                  <  1:39949/141‑1 (MQ=255)
                                                                                      aCGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTTAATACtta                                              <  2:293445/141‑1 (MQ=255)
                                                                                       cGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACttat                                             >  2:127580/1‑141 (MQ=255)
                                                                                       cGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACttat                                             >  2:99347/1‑141 (MQ=255)
                                                                                          tAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAg                                          <  1:380720/141‑1 (MQ=255)
                                                                                            gTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTc                                        >  1:147097/1‑141 (MQ=255)
                                                                                              tGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGa                                      <  1:81069/141‑1 (MQ=255)
                                                                                               ggTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGAt                                     <  1:347517/141‑1 (MQ=255)
                                                                                                      ggaCAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCAGTCAACATAACGGTGAATACTTATTAGTCGATTTAGTaa                              >  2:10542/3‑141 (MQ=255)
                                                                                                          aaaaaGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCAc                          <  1:278101/141‑1 (MQ=255)
                                                                                                              aGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACACAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTgg                      >  1:387618/1‑141 (MQ=255)
                                                                                                                    ggggATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCgtg                <  2:309683/141‑1 (MQ=255)
                                                                                                                    ggggATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCgtg                <  2:239078/141‑1 (MQ=255)
                                                                                                                         tCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCGTGTACtt           <  2:118516/141‑1 (MQ=255)
                                                                                                                             ttAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCGTGTACtttttt       <  2:251971/141‑1 (MQ=255)
                                                                                                                                  aCTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCGTGTACTTTTTTCCttt  <  1:168556/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                        
TGGATTAAGAGATAAAACTAATTGGATAAGACATTAAATAGACGCTGTTTAAAAATACCACAGAAAAAGCTGTAGATAGTGTTGGAACGATAGTTGGTGAAGGTACAAAAAGTATTGGGGATCATTTAAAACTAATGAAACGGGAGTGGTAAATGTTGCTTTGCGATGTCAGAGTCATTTATAAAAATCCGAAATACAAAGTCATTCAACATAACGGTGAATACTTATTAGTCGATTTAGTAAGCACTTGGTTCGTGTACTTTTTTCCTTT  >  CP000730/659954‑660224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑