Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,679,462 (A)8→7 100% intergenic (+334/‑55) USA300HOU_2535 → / → USA300HOU_2536 hypothetical protein/possible secretory antigen

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,679,4550A.97.0% 139.8 / ‑1.6 33intergenic (+327/‑62)USA300HOU_2535/USA300HOU_2536hypothetical protein/possible secretory antigen
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (17/15);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.90e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  CP000730/2679318‑2679587
                                                                                                                                           |                                                                                                                                    
gTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAATTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTaaaa                                                                                                                                   >  1:102182/1‑141 (MQ=255)
           tctattaattGTTAAATACATGAATTTCTACATTTTATGAAATAATCCATTTTTATTACGATTCAACACTTTATATGACATCTTCATTACAGTTACTTTTATTGTTGATTGGTTAAATTG‑‑TATTATAAAAAAATTTGTTAt                                                                                                                       <  2:9720/138‑1 (MQ=255)
           aCAATTAACTATTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTAt                                                                                                                       <  2:9639/141‑1 (MQ=255)
            cAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATc                                                                                                                      <  1:375635/141‑1 (MQ=255)
                 aattGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑‑AAAAAATTTGTTATCATAAtt                                                                                                                >  1:192348/1‑141 (MQ=255)
                  attGTTAAATACATAAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAAtt                                                                                                                >  1:260111/1‑141 (MQ=255)
                     gTTAAATACATGAATTTCTACCTTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAAc                                                                                                             <  1:181257/141‑1 (MQ=255)
                       tAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGt                                                                                                           <  1:211832/141‑1 (MQ=255)
                          aTACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGa                                                                                                        >  1:314038/1‑141 (MQ=255)
                              aTGAATTTCTACATTTTGTTAAAAAAGCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                    <  2:394617/141‑1 (MQ=255)
                              aTGAATTTCTACATTTTATGAAAAAATCCATTTTTATTATAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                    >  2:121127/1‑141 (MQ=255)
                                      cTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaaa                                                                                            <  1:177752/141‑1 (MQ=255)
                                       tACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaaaa                                                                                           <  1:324434/141‑1 (MQ=255)
                                        acaaaaaaagAAAAAATCGGATTTTATTAAAATTCAACACTTTATATGACAACTTCATTAAAGTTACTTTTATTGTTGATTGCTTAAAAA‑‑AAAAAAAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAt                                                                                          <  2:394786/132‑1 (MQ=255)
                                        aCATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAt                                                                                          <  2:238083/141‑1 (MQ=255)
                                         cATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAtt                                                                                         <  1:308038/141‑1 (MQ=255)
                                                  aaaaaaTCCATTTTTATTACAATTCAACACTTTATAAGAAAAATTTTTTAATATTTATTTTATTTTTGATTTCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGga                                                                                <  2:278579/141‑1 (MQ=255)
                                                              tttATTACACTTCCACACTTTATATGACACCTTCCTTACTGTTACCTAAATGTCAACACTATCATTGCAATTTCTAACAAAATTTGTTCTCGTAATTAACTTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGa                                                                    <  2:380187/141‑1 (MQ=255)
                                                                 attaCAATTCAACACTTTATATGACCACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAata                                                                 <  2:394692/141‑1 (MQ=255)
                                                                 attaCAATTCAACACTTTATATGACAACTTCATTACCGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAata                                                                 <  2:394757/141‑1 (MQ=255)
                                                                        ttCAACACTGTATATGACAAGTTCATTACAGCTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATaaaaaa                                                          >  2:299359/1‑140 (MQ=255)
                                                                        tctaaCACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCCTAATTAACGTTGAATAAAGAAAAAAATTAAATTGGTGGATAAAAATGGAGTATAAAAAg                                                          >  2:299419/4‑141 (MQ=255)
                                                                             cacTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACt                                                     >  1:316698/1‑141 (MQ=255)
                                                                                   atatGAAAACTTCTGTACATGTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAAAAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCg                                               <  1:173371/141‑1 (MQ=255)
                                                                                               cATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGc                                   >  2:376373/1‑141 (MQ=255)
                                                                                               cATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGc                                   >  2:344607/1‑141 (MQ=255)
                                                                                                aTTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATAATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCt                                  >  1:92366/1‑141 (MQ=255)
                                                                                                   aCAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCtttt                               >  2:345535/1‑141 (MQ=255)
                                                                                                           ttttATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACt                       >  2:106295/1‑141 (MQ=255)
                                                                                                                ttgttgATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTtct                  >  2:318645/1‑141 (MQ=255)
                                                                                                                    tgATTGCTTACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcagc              >  1:117003/1‑141 (MQ=255)
                                                                                                                           ttACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTATCGATGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc       >  2:65023/1‑141 (MQ=255)
                                                                                                                           ttACATTG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc       >  2:320268/1‑141 (MQ=255)
                                                                                                                                ttG‑‑TTTTCTAAAAAAATTTGTTATCATAATTAACGTTGGATACAGAAAATCCGTCACTGGGGAGATAAAAATGGAATATAAAAAGATACTGATCGGCTTGTGAGTGGCGTTGGCAGTACTATCCTCAGCAGAGGTCACTTa  >  1:132119/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                    
GTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  CP000730/2679318‑2679587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: