Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,455,698 2 bp→AT 100% coding (1216‑1217/1260 nt) USA300HOU_2315 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,455,6980CA93.6% 135.1 / 5.1 47coding (1216/1260 nt)USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (23/21);  minor base . (1/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 6.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01
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.
*CP0007302,455,6990AT100.0% 134.6 / ‑6.5 47H406L (CAT→CTT) USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (24/22);  total (24/23)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  CP000730/2455565‑2455826
                                                                                                                                     ||                                                                                                                               
aTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaa                                                                                                                          >  1:376853/1‑141 (MQ=255)
 tCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAAGAAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaa                                                                                                                         >  1:367206/1‑141 (MQ=255)
       aaaCAAGCACACCAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTg                                                                                                                   <  2:223307/141‑1 (MQ=255)
        atcAATCACCACAAAGGGACGACTCAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGATAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTga                                                                                                                  <  2:501905/139‑1 (MQ=255)
             acaccacAAAGTGACGATTTAACAAACAATTCAAAGGAAGAGTAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCACAAAAA‑TTATCGAAAAAACTGAAGAAc                                                                                                             <  2:431757/140‑1 (MQ=255)
              caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCAGTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACa                                                                                                            <  2:220128/141‑1 (MQ=255)
               accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACaa                                                                                                           >  2:526738/1‑141 (MQ=255)
                 cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGTGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATc                                                                                                         >  2:123282/1‑141 (MQ=255)
                   caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCtt                                                                                                       <  1:364869/141‑1 (MQ=255)
                     aaGTGACGATTTAACAAACGACTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa                                                                                                     <  1:375770/141‑1 (MQ=255)
                      aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                    <  1:162111/141‑1 (MQ=255)
                        tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAAAAATCTTCAGAt                                                                                                  >  2:374004/1‑141 (MQ=255)
                           agATTTAAAAAACGATACAAATGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                               <  2:497940/140‑1 (MQ=255)
                                      aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAataata                                                                                    <  1:279853/141‑1 (MQ=255)
                                         aTTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATACAAACAAATAATAACa                                                                                 <  1:516731/141‑1 (MQ=255)
                                               aTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcgc                                                                           >  2:29373/1‑141 (MQ=255)
                                                             gtgccaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                             <  1:238540/136‑1 (MQ=255)
                                                             gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACATACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACctct                                                             <  1:490769/141‑1 (MQ=255)
                                                             gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                             <  1:342912/141‑1 (MQ=255)
                                                                 aaTCATTACAAGAACCTTCCACATATAAAGAAGACCTACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTccccattgac                                                         <  2:6847/141‑8 (MQ=255)
                                                                  aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                        >  1:207090/1‑141 (MQ=255)
                                                                      ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                    >  1:546391/1‑141 (MQ=255)
                                                                        gaaaGAACCTGCGACCTATAAAGAAGACAGACGTTCATCAGTTGTAAGTGATGC‑CAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATGATAACAAAGCGCGTGCTAGTACCTCTTAAAAAgatgt                                                  >  2:83781/2‑140 (MQ=255)
                                                                        aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                  >  1:359068/1‑141 (MQ=255)
                                                                         aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCACATAAAAAgatgat                                                 >  2:399363/1‑141 (MQ=255)
                                                                                cTGCGGCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                          <  2:515039/141‑1 (MQ=255)
                                                                                cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                          >  2:281293/1‑141 (MQ=255)
                                                                                 tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAGACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  1:303648/141‑1 (MQ=255)
                                                                                 tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         >  2:199510/1‑141 (MQ=255)
                                                                                 tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGGAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  1:204374/141‑1 (MQ=255)
                                                                                  gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                        >  2:578511/1‑141 (MQ=255)
                                                                                  gCGAATTAAAAACAAGACAGACTTTCATCAGTTGAAATAGAAGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATCACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                        <  2:372206/141‑1 (MQ=255)
                                                                                  ctcaCTTACACATAATACAGACGTTCATCAGTTGTAATTAATACA‑AAAAAAATATCGAAAAATCTGAAGAACAATCTTCAGATAAAAACAAATAATAACAATGCGCTTGCTAGTACCTCTTTAAAAGATGATGCTAGCAAg                                        <  2:419874/138‑1 (MQ=255)
                                                                                     aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                     >  2:409734/1‑141 (MQ=255)
                                                                                      cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                    <  1:580420/141‑1 (MQ=255)
                                                                                         ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAGAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                 >  1:464258/1‑141 (MQ=255)
                                                                                          taAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                                >  2:35522/1‑141 (MQ=255)
                                                                                           aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCAGCGCTTTTct                               >  2:94919/1‑141 (MQ=255)
                                                                                           aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTct                               >  2:555634/1‑141 (MQ=255)
                                                                                                  acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCAGCGCTTTTctatactaa                        >  1:272090/1‑140 (MQ=255)
                                                                                                  acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat                        >  2:5052/1‑141 (MQ=255)
                                                                                                     gacTTTCATCAGTTGTAATTGATGC‑CAAAAAATGATCGACAAAACTGAAGAACAATCTTCAGATAAAAATAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                     <  2:316453/141‑1 (MQ=255)
                                                                                                     gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                     <  1:353089/141‑1 (MQ=255)
                                                                                                          tcatcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGGTGATGCTAGCAAGGGGTTTTCTATAGTATATattgtt                >  1:174356/1‑141 (MQ=255)
                                                                                                            atcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt              >  1:101264/1‑141 (MQ=255)
                                                                                                               aGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTTCCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCt           <  2:7797/141‑1 (MQ=255)
                                                                                                                        tGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAGGCGCTGGCTAGTACCTCTTCAAAAGAAGATGCTAGCAACCGCTTTTCTATCCTATATATTATTTTTCTAAAATTTTa  >  2:107998/1‑141 (MQ=255)
                                                                                                                                     ||                                                                                                                               
ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  CP000730/2455565‑2455826

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: ‑