Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,455,698 C→A 100% H406N (CAT→AAT) ‡ USA300HOU_2315 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,455,6980CA76.9% 68.0 / 23.1 47H406N (CAT→AAT) ‡USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (5/5);  new base A (18/15);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.31e-01
Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch.

TAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  CP000730/2455571‑2455831
                                                                                                                               |                                                                                                                                     
tAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACt                                                                                                                         >  1:68235/1‑141 (MQ=255)
tAAACAAGCACCACAAAGTGAAGATTTAACAAACGATTCAAATGACGATGGAATAGAGCAATCATTAAAAGAACCTGCGAGTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATTCAAAAAAATTATCGAAGAAGCt                                                                                                                         >  1:583146/1‑141 (MQ=255)
  aaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACAGATCGAAAAAACTg                                                                                                                        >  2:402410/1‑141 (MQ=255)
      aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaagaa                                                                                                                   <  1:28334/141‑1 (MQ=255)
         accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACa                                                                                                                 <  2:27467/141‑1 (MQ=255)
           cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATc                                                                                                              >  1:542971/1‑141 (MQ=255)
             caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCtt                                                                                                            >  1:529689/1‑141 (MQ=255)
             caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCtt                                                                                                            >  2:467703/1‑141 (MQ=255)
                  tGACGATTGAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                       <  1:110813/141‑1 (MQ=255)
                         ttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                                 <  1:374998/141‑1 (MQ=255)
                               accGATTCAAATGAAGACAAAATAGAGGAATCATTAAACGATCCTGCGACTTATAAAGAAGACAGATGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaataa                                                                                           <  2:455860/139‑1 (MQ=255)
                                 agATTCAAATGAAGATGAAACAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATAATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAAtaataa                                                                                        <  2:537021/140‑1 (MQ=255)
                                  gATTCAAATGAAGATGAAACAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAAc                                                                                       <  1:18539/141‑1 (MQ=255)
                                    ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACa                                                                                      >  1:145292/1‑141 (MQ=255)
                                     tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGGAGACAAACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaaa                                                                                    <  2:218742/141‑1 (MQ=255)
                                        aaTGAAGATGAAATAGCGCAATCATTAAAAGAAGCTGCGACTTATAAAGAAGATAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                  <  2:500573/141‑1 (MQ=255)
                                        aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                  >  2:427304/1‑141 (MQ=255)
                                        aaTAAAGAAGAAAAAGAGCAATCATTAAAAGAACCTGCAACTTATAAAGAAGACAGACGTTCATCAGTTGAAATAAAAAAAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcg                                                                                 <  2:542832/141‑1 (MQ=255)
                                          tGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCt                                                                               <  1:166431/141‑1 (MQ=255)
                                              gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                           <  1:587174/141‑1 (MQ=255)
                                                 gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGGCAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt                                                                        <  1:322128/141‑1 (MQ=255)
                                                      agatcactgatgaaaaGAACCTGAGACTTACAAAGAATACAGACTTTCATCAGTTGTAACTGATGCAAAAAAATTATCTAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                   <  2:356286/129‑1 (MQ=255)
                                                       gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                                  >  1:421427/1‑141 (MQ=255)
                                                           aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTaa                                                               >  1:443433/1‑141 (MQ=255)
                                                             tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                             <  1:520430/141‑1 (MQ=255)
                                                             tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa                                                            >  1:128690/1‑141 (MQ=255)
                                                                ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgaa                                                         >  2:215703/1‑140 (MQ=255)
                                                                   aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                       >  1:251373/1‑141 (MQ=255)
                                                                     aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc                                                    >  1:176662/1‑141 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAGAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTaa                                                 >  2:411365/1‑140 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                 <  2:68235/141‑1 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                 >  1:284641/1‑141 (MQ=255)
                                                                         ccTGCGACTTATAACGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                                >  2:413992/1‑141 (MQ=255)
                                                                         ccTGCGACTTATAAAGAAGACAGACGTACATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAGCAAATAATAACAAAGGGCTCGCTAGTACCTCTTAAAAAAATGATGCTaaa                                                >  2:416720/1‑139 (MQ=255)
                                                                          ctacGACTCAAAAAGAAGAAAGACGTTCATCAGTTGAAAAAAAAAAAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                               <  2:230934/138‑1 (MQ=255)
                                                                             cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACGCCTTAAAAAAATGATGCTAGCAAgg                                            >  1:107247/1‑140 (MQ=255)
                                                                               aCTTATAAAGAAGACCGACGTTCATCAGTTGTAATTGATGCAATAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATATCAAAGCGCTTGCTAGTACCTCTTAAAAAGATGAGGCTAGCATgcgc                                          <  1:430522/141‑1 (MQ=255)
                                                                               aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                          <  2:251828/141‑1 (MQ=255)
                                                                                  tataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgtaat                                       <  2:6040/141‑5 (MQ=255)
                                                                                  tataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCttt                                       <  1:144505/141‑1 (MQ=255)
                                                                                        gaagaCAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                                 >  1:107657/1‑141 (MQ=255)
                                                                                           gacagacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGGTAGCAACCGATTTTctatacta                              >  2:393948/1‑141 (MQ=255)
                                                                                                acGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat                         >  1:213092/1‑141 (MQ=255)
                                                                                                        caGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                 <  2:24142/141‑1 (MQ=255)
                                                                                                            tGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAAATATTATTTTTCTaaa             >  1:4996/1‑141 (MQ=255)
                                                                                                             gTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaaa            >  2:188147/1‑141 (MQ=255)
                                                                                                               aaTTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt          >  1:376172/1‑141 (MQ=255)
                                                                                                                        gaaaaaaaGTATCGAAAAAACTGAAGATCAATTTTCAGATAAAAATAAATAATAACAATGCGCTTGCTAGTACCTCTTAAAAAGATTATGCTAGCCAGCGCTTTTCTATACTCTATATTATTTTTCTAAAATTTTAACAcc  <  2:258512/139‑1 (MQ=255)
                                                                                                                               |                                                                                                                                     
TAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  CP000730/2455571‑2455831

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: