Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 89,761 G→A 10.8% intergenic (‑805/+1940) USA300HOU_0086 ← / ← USA300HOU_0089 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073089,7610GA10.8% 102.1 / 3.2 37intergenic (‑805/+1940)USA300HOU_0086/USA300HOU_0089hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (16/17);  new base A (2/2);  total (18/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

AATTTATTTTCAGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGTTAGACCTTCAGAA  >  CP000730/89629‑89901
                                                                                                                                    |                                                                                                                                            
aaTTTATTTTCAGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGa                                                                                                                                      >  1:136889/1‑141 (MQ=255)
     atttTCAGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATAACTTCGGAATTGa                                                                                                                                 >  1:122377/1‑141 (MQ=255)
     atttTCAGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATAACTTCGGAATTGa                                                                                                                                 >  1:122369/1‑141 (MQ=255)
          cAGAATCCGGTCATCATTTGTATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTg                                                                                                                            <  1:115505/141‑1 (MQ=255)
           aGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGc                                                                                                                           >  1:107326/1‑141 (MQ=255)
              aTCCCGTCATCATTTTGATGCAATATTATTTCTCAAAGAATATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGa                                                                                                                        <  2:401535/141‑1 (MQ=255)
                ccGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGaaa                                                                                                                      <  2:37796/141‑1 (MQ=255)
                           tttGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCaaa                                                                                                           >  2:216369/1‑141 (MQ=255)
                                tGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGa                                                                                                      <  1:26791/141‑1 (MQ=255)
                                 gCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGaa                                                                                                     >  2:400059/1‑141 (MQ=255)
                                   aaTATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGa                                                                                                   >  1:384486/1‑141 (MQ=255)
                                          tttCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGtt                                                                                            <  1:115268/141‑1 (MQ=255)
                                            tctcAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTtaa                                                                                          >  2:250445/1‑141 (MQ=255)
                                                             caTTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAAttaacattttt                                                                         <  1:354631/141‑11 (MQ=255)
                                                                 aCAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTca                                                                     <  1:343721/141‑1 (MQ=255)
                                                                     aataatGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTcaagaa                                                                 <  2:385570/141‑1 (MQ=255)
                                                                          tGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAg                                                            <  2:418524/141‑1 (MQ=255)
                                                                              tatatTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCtt                                                        >  2:276023/1‑141 (MQ=255)
                                                                              tatatTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCtt                                                        >  1:339799/1‑141 (MQ=255)
                                                                                 attatACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATAACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTaaa                                                     <  2:122377/141‑1 (MQ=255)
                                                                                 attatACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATAACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTaaa                                                     <  2:122369/141‑1 (MQ=255)
                                                                                   tataCCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACTTTACAAGCTTTAaga                                                   >  2:184930/1‑141 (MQ=255)
                                                                                    ataCCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAagag                                                  >  2:213207/1‑141 (MQ=255)
                                                                                    ataCCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAagag                                                  <  1:262943/141‑1 (MQ=255)
                                                                                      aCCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGAt                                                <  2:230705/141‑1 (MQ=255)
                                                                                          tttGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGtt                                            <  1:62995/141‑1 (MQ=255)
                                                                                                 aaGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATtata                                     >  1:375080/1‑141 (MQ=255)
                                                                                                       atCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGa                               >  2:174553/1‑141 (MQ=255)
                                                                                                       aacATGATATAAATAATGTGGTTGATTATGACTTCGGAACTGATTTTGCAGCAATTGCAATCCAAAAAGAGGACATAGTTAATAAAAATGTTGATGTTTTTCAACAAAACAAGCTTAAAGAGATTGTTCATTATAGCAGGa                               >  2:99769/3‑141 (MQ=255)
                                                                                                          aTGATATAAATAATTTGATTGATTATGAGTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATa                            >  2:386276/1‑141 (MQ=255)
                                                                                                            gaaataaataaTTTGATTGATTATGACTTCGGAATTGATTCTGCAGAAAGCGCAATCAAAAATGAAGACATAGTTAATAACAATGTTAATTTTTTTCCACAACACAGGCTTAAAGAGATTGTTAAATATAGAAGGAATAga                          >  2:102106/4‑140 (MQ=255)
                                                                                                            gATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAgt                          >  2:318689/1‑141 (MQ=255)
                                                                                                                   ataatTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGAtt                   <  1:216369/141‑1 (MQ=255)
                                                                                                                       tttGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGt               <  1:78695/141‑1 (MQ=255)
                                                                                                                       tttGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGt               <  1:216192/141‑1 (MQ=255)
                                                                                                                              gattATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGTTAGACCt        <  1:55709/141‑1 (MQ=255)
                                                                                                                                ttATGACGTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGTTAGACCTTc      <  1:71821/141‑1 (MQ=255)
                                                                                                                                    gACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGTTAGACCTTCAGaa  >  2:296886/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                            
AATTTATTTTCAGAATCCGGTCATCATTTTGATGCAATATTATTTCTCAAAGAAGATACAACATTACAAAATAATGTATATATTATACCTTTTGGACAAGCATATCATGATATAAATAATTTGATTGATTATGACTTCGGAATTGATTTTGCAGAAAGAGCAATCAAAAATGAAGACATAGTTAATAAAAATGTTAATTTTTTTCAACAAAACAGGCTTAAAGAGATTGTTAATTATAGAAGGAATAGTGTAGATTACGTTAGACCTTCAGAA  >  CP000730/89629‑89901

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