Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 2,455,698 2 bp→AT 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
*CP0007302,455,6980CA92.6% 84.2 / 1.3 28coding (1216/1260 nt)USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (6/19);  minor base . (0/2);  total (6/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01
*CP0007302,455,6990AT92.9% 84.1 / ‑5.5 29H406L (CAT→CTT) USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base T (6/20);  total (6/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT  >  CP000730/2455566‑2455833
                                                                                                                                    ||                                                                                                                                      
tCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGaaa                                                                                                                                >  2:80292/1‑141 (MQ=255)
            gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAAc                                                                                                                    <  1:168006/141‑1 (MQ=255)
                 acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCt                                                                                                               <  1:9603/141‑1 (MQ=255)
                   aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTc                                                                                                             <  2:236607/141‑1 (MQ=255)
                     aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTAATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                           <  1:138476/141‑1 (MQ=255)
                       tcaagATGTAACAAATGAATCAAATGAAAATGAAAAAGAGCAATCATTAAAAGCACCTTCGCCCTATAAAGAAGACAGACGTTCATCAGTTGAAAAAAAAAAAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                         <  2:160030/137‑1 (MQ=255)
                       tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                         <  1:67017/141‑1 (MQ=255)
                        aaCGATTTAACAAACGATTCAAATGAAGAAGAAATAGAGCAATCATAAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAAAAATAAAAAAAACTGAAGAACAATCTTCAGATa                                                                                                        <  2:40095/140‑1 (MQ=255)
                         aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa                                                                                                       >  2:225390/1‑141 (MQ=255)
                                 aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaat                                                                                               <  1:46380/141‑1 (MQ=255)
                                 aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaat                                                                                               <  1:182319/141‑1 (MQ=255)
                                     aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAataata                                                                                           >  1:163955/1‑141 (MQ=255)
                                                 aaGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTg                                                                               <  1:51005/141‑1 (MQ=255)
                                                    atcaaaTAGAACAATCATTAAAACAACCTTCAACTTATAAAGAATACAAACGTTCATCAGTTGTAATTGATGCAAAAAAATAATCAAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                            <  2:282232/138‑1 (MQ=255)
                                                    aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                            <  2:187271/141‑1 (MQ=255)
                                                             agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt                                                                   >  2:33089/1‑141 (MQ=255)
                                                                 aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATAAAAACAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                               <  2:245921/141‑1 (MQ=255)
                                                                 aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAAAAGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                               <  2:120779/141‑1 (MQ=255)
                                                                   cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg                                                             <  2:58559/141‑1 (MQ=255)
                                                                        aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                        >  1:46367/1‑141 (MQ=255)
                                                                             aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATAGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                   <  2:239093/141‑1 (MQ=255)
                                                                                 gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTAATGCAAAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                               <  1:32774/141‑1 (MQ=255)
                                                                                        ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                        <  1:214105/141‑1 (MQ=255)
                                                                                           aagaagACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta                                     <  2:229180/141‑1 (MQ=255)
                                                                                           aagaagACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCGTTTAAAAAGATGATGCTAGCAAGCGCTTTTcta                                     >  1:90884/1‑141 (MQ=255)
                                                                                                             caGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                   <  2:46367/141‑1 (MQ=255)
                                                                                                                      ttGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt          <  1:224383/141‑1 (MQ=255)
                                                                                                                       tGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTa         <  2:8968/141‑1 (MQ=255)
                                                                                                                               aaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAACAGATGATGCTAGCCAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCct  <  1:257685/141‑1 (MQ=255)
                                                                                                                                    ||                                                                                                                                      
TCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT  >  CP000730/2455566‑2455833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: