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
*CP0007302,455,6980CA85.4% 125.3 / 20.4 48coding (1216/1260 nt)USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (25/16);  minor base . (4/3);  total (29/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.
*CP0007302,455,6990AT100.0% 144.9 / NA 51H406L (CAT→CTT) USA300HOU_2315hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (29/22);  total (29/22)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACA  >  CP000730/2455568‑2455829
                                                                                                                                   ||                                                                                                                                  
aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGaaaaa                                                                                                                          <  2:389097/141‑1 (MQ=255)
 gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGaaaaaa                                                                                                                         >  1:287199/1‑141 (MQ=255)
 gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGGTGTAATTGATGCAAAAAAATTATCGaaaaaa                                                                                                                         >  1:139012/1‑141 (MQ=255)
        aaGCACCACAAAGTGACAATTAAACAAACGATCCAAATGAAAATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGATGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTgaaga                                                                                                                  <  1:67782/141‑1 (MQ=255)
              cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACactg                                                                                                            >  1:315633/1‑138 (MQ=255)
               acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAAAAATCt                                                                                                           >  1:215551/1‑141 (MQ=255)
               acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGGTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCt                                                                                                           >  1:115474/1‑141 (MQ=255)
                 aaaGGGACGATTTAACAAACGATTCAAAGGAAGATGAAATAGAGCAATCATTAAAAGAAGCTGCGACGTATAAACAAGACAGACGTACATCAGTTGTAATTGATGCAAAAAAATTATCGAAAATACTGAAGAACAATCTTc                                                                                                         <  2:187576/141‑1 (MQ=255)
                    gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAATAACAATCTTCAGa                                                                                                      >  1:40278/1‑141 (MQ=255)
                        cGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCACAAG‑‑ATAATTTATAGTCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                                  >  1:389975/1‑141 (MQ=255)
                         gATTTAACAAACTATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGCACAGTCTTCGGATaacc                                                                                                 <  2:185135/141‑3 (MQ=255)
                         gATATAACAAACGATTCAAAGGAAGATGAAATAGATCAATCATTAAAAGAACCTGCGACTTATAAACAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa                                                                                                 <  2:296809/141‑1 (MQ=255)
                           tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCATAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                               >  1:328360/1‑141 (MQ=255)
                           tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                               >  2:13416/1‑141 (MQ=255)
                            ttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACa                                                                                              >  2:55921/1‑141 (MQ=255)
                                           aaTGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAGAAAATAACAAAacg                                                                               >  2:23555/1‑141 (MQ=255)
                                                 gATGGAATAGAGCAATGATTAAAAGAACCTGCCACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                         <  2:220610/141‑1 (MQ=255)
                                                 aaTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACATAGCGCTTGCt                                                                         <  2:269846/140‑1 (MQ=255)
                                                  aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCgctagcta                                                                        >  2:198057/1‑141 (MQ=255)
                                                  aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa                                                                        >  1:385689/1‑141 (MQ=255)
                                                       aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc                                                                   >  1:63196/1‑141 (MQ=255)
                                                         agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc                                                                 <  2:132066/141‑1 (MQ=255)
                                                          gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                                <  1:376576/141‑1 (MQ=255)
                                                                     aaaaGAACCTGCGACTTATAAAGAATACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                     <  2:268367/141‑1 (MQ=255)
                                                                     aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                     >  2:301116/1‑141 (MQ=255)
                                                                      aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTGATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAgatgat                                                    >  2:213537/1‑141 (MQ=255)
                                                                      aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACCATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat                                                    >  1:255989/1‑141 (MQ=255)
                                                                      aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAAACATCAGATAAAAACAAATAATAACAAAGCACTAGCTAGTACCTCTTAAAAAgataat                                                    >  2:15203/1‑141 (MQ=255)
                                                                       aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTCGCTAGTACGTCTTAAAAAGatgatg                                                   >  1:362092/1‑141 (MQ=255)
                                                                         gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt                                                 >  2:117688/1‑141 (MQ=255)
                                                                         aaaacTGTGACTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTGCAGACAAAAACAAATAATAACAAAGCTCTTGCTAGTACCTCTTAAAAAGATGATGCt                                                 <  1:306117/137‑1 (MQ=255)
                                                                              tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                            <  2:386398/141‑1 (MQ=255)
                                                                              tGCGACTTATAAAGAAGACAGACGGTCAACAGTCGTAATTGATTCAAAAAAATTATCGAAAAAACTGAAGCACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                            <  1:53345/141‑1 (MQ=255)
                                                                              tGCGACTTAAAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                            <  2:153105/141‑1 (MQ=255)
                                                                               gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                           >  1:209057/1‑141 (MQ=255)
                                                                                   cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                       >  1:248080/1‑141 (MQ=255)
                                                                                   cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                       >  2:215817/1‑141 (MQ=255)
                                                                                        aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAATTGATGCTAGCAAGCGCTTTTct                                  >  1:247040/1‑141 (MQ=255)
                                                                                             agacagacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAACGCTTTTctattct                             >  1:16607/1‑141 (MQ=255)
                                                                                             agacagacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTCTTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact                             <  1:77216/141‑1 (MQ=255)
                                                                                                  gacGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                        <  1:329829/141‑1 (MQ=255)
                                                                                                    cGTTCATCAGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCTTTTCTATACTATAtatt                      >  1:357012/1‑141 (MQ=255)
                                                                                                        catcaGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttt                  >  1:256597/1‑141 (MQ=255)
                                                                                                        catcaGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACACTCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGGTGCTAGCCAGCGCATTTCTATACTATATATTAttt                  >  1:111188/1‑141 (MQ=255)
                                                                                                         attaGTTGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATTTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt                 <  1:86299/138‑1 (MQ=255)
                                                                                                              atGTAATTGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaa            <  2:303790/140‑1 (MQ=255)
                                                                                                                  aaTTGATGCAAAAAAATTATCGAAAACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt        <  1:3721/141‑1 (MQ=255)
                                                                                                                     tGATGCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTATTAAAAAGATGATGCTAGCAAGCGCTTTTATATAAAATATATTATTTTTATAAAATTTTa     >  2:258304/1‑141 (MQ=255)
                                                                                                                      tttatgaaaaaaaaTTATCGCAAAATCTGAAGAACAATCTTCAGATAAATATAAATAATAACAAAGCGCTTGCTAGTACCTCTTCAATAGATGATTCTAGCAAGCGCTTTTCTTTACTATATATTATTTTTCTAAACtttt      <  2:337697/133‑1 (MQ=255)
                                                                                                                          tgcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAAGAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAaca  <  2:139012/137‑1 (MQ=255)
                                                                                                                          agaaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAaca  <  2:287199/137‑1 (MQ=255)
                                                                                                                                   ||                                                                                                                                  
AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACA  >  CP000730/2455568‑2455829

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: