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
*CP0007302,455,6980CA90.6% 84.1 / 3.3 32coding (1216/1260 nt)USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (11/17);  minor base . (2/1);  total (13/19)
Fisher's exact test for biased strand distribution p-value = 5.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
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% 96.4 / ‑6.5 33H406L (CAT→CTT) USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (13/19);  total (13/20)
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.

ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  CP000730/2455565‑2455831
                                                                                                                                     ||                                                                                                                                    
accAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGaa                                                                                                                               <  2:166275/139‑1 (MQ=255)
            aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaagaa                                                                                                                   >  1:91967/1‑141 (MQ=255)
            aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaagaa                                                                                                                   <  2:268206/141‑1 (MQ=255)
              caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGCAGAACa                                                                                                                 >  2:332674/1‑141 (MQ=255)
                       gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGa                                                                                                        <  1:58064/141‑1 (MQ=255)
                        tGACTATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                       <  1:368645/141‑1 (MQ=255)
                         gACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATa                                                                                                      <  1:87077/141‑1 (MQ=255)
                                      aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAataata                                                                                         >  1:307108/1‑141 (MQ=255)
                                             aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACGATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                  >  1:186263/1‑141 (MQ=255)
                                                tGAAGCTGAAATAAAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATAATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCt                                                                               <  2:150933/141‑1 (MQ=255)
                                                tGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcgca                                                                               >  1:93457/1‑140 (MQ=255)
                                                  aaaaTGAAATAGAGCAATAATTAAAAGAACCGGCGAATTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTg                                                                             <  2:135418/138‑1 (MQ=255)
                                                          aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTAcc                                                                     <  1:155564/141‑1 (MQ=255)
                                                          aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc                                                                     >  1:246652/1‑141 (MQ=255)
                                                              agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCtt                                                                 >  1:310940/1‑141 (MQ=255)
                                                                 aagcATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                              <  1:2847/138‑1 (MQ=255)
                                                                 aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACATACGTTCATCCGTTATAATTTATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa                                                              <  1:366188/141‑1 (MQ=255)
                                                                      tgaaaaGAACCCGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCATCAGACAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTACAAAgat                                                         <  1:284957/139‑1 (MQ=255)
                                                                         aaaGAACCTGCGACGGATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAATACGTCTTAAAAAgatgat                                                      >  2:32288/1‑141 (MQ=255)
                                                                                cTGCGACTTATATATAAGACAGCTCTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACACATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                               <  2:333580/141‑1 (MQ=255)
                                                                                 ggcaacgtaaaaaGAAGACAGACGGTCATCAGTTGTAATTGAAGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                              <  2:103713/131‑1 (MQ=255)
                                                                                    gACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg                                           <  1:158621/141‑1 (MQ=255)
                                                                                     aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                          <  1:275586/141‑1 (MQ=255)
                                                                                      attATAAAGAAGAGAGACGTACATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                         <  2:71328/140‑1 (MQ=255)
                                                                                            aagaagACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta                                   >  2:120959/1‑141 (MQ=255)
                                                                                                agacagacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGATAGTCCCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact                               >  2:141821/1‑141 (MQ=255)
                                                                                                  acagacGTTCATCAGTTGTAATTGATATAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctaaactaa                             >  2:80134/1‑140 (MQ=255)
                                                                                                      acGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat                         >  1:229182/1‑141 (MQ=255)
                                                                                                      acGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat                         <  2:94726/141‑1 (MQ=255)
                                                                                                         ttCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAGAtattat                      >  2:232885/1‑141 (MQ=255)
                                                                                                            atcaGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTTCCACGTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                   <  1:332674/141‑1 (MQ=255)
                                                                                                               aGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAACAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCt                <  2:237513/141‑1 (MQ=255)
                                                                                                                              aaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTATCAcc  <  2:258185/139‑1 (MQ=255)
                                                                                                                                     ||                                                                                                                                    
ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  CP000730/2455565‑2455831

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: