Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,028,583 G→T 100% A21D (GCC→GAC)  USA300HOU_1882 ← hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,028,5830GT96.3% 101.4 / ‑4.2 42A21D (GCC→GAC) USA300HOU_1882hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base T (17/22);  total (19/23)
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
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCA  >  CP000730/2028449‑2028719
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aTAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCaata                                                                                                                                     <  1:517227/140‑1 (MQ=255)
        ccTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTAAATAAACTACTACAGATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATGTGTAGTAAAAATTGTCAATAATCATTaa                                                                                                                             >  2:253/1‑140 (MQ=255)
         cTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTATAAATAAtaattaat                                                                                                                            >  1:398648/1‑140 (MQ=255)
                      cAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACGCATCCCACTAATAGAACGAGTAAAAAGCCAATTTTGTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCCGTAAAAATGa                                                                                                               >  2:39976/1‑140 (MQ=255)
                        aaaGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATc                                                                                                             <  1:187938/140‑1 (MQ=255)
                          aGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCaa                                                                                                           >  1:491044/1‑140 (MQ=255)
                          aGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGAACaa                                                                                                           >  2:395975/1‑140 (MQ=255)
                          aGGCCACATATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGAAGTAAAAATTGTCAATAATCATTAATGCAGTACAAATGATCaa                                                                                                           >  1:343601/1‑140 (MQ=255)
                              caactATGTTATGAAAATAAAGATATCCTACATAAACTAATACACATCACAATTATACAACTAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  1:128125/136‑1 (MQ=255)
                              cACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  2:338193/140‑1 (MQ=255)
                              cACGTATTTTATGAAAATAAAGATATACTACATTAACCAATACACATCCCAATAATAGAACGACTAAAAAACCAAAATATTCAAATAATATGTAGTAAAAATTGTCAATAATCATTAATGTAGTAAAAATGATCAACAtt                                                                                                       <  1:357858/140‑1 (MQ=255)
                              cACGTACTTTATGAAAATAAAGATATCCTACATAAACTATTTCAGACTCCACTATTAGAAGTAGTAAAAAGTCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  2:30991/140‑1 (MQ=255)
                                cGTATTTTATGATAATAAAGATATTCTTCATAAACTAATACACATCGCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTg                                                                                                     <  1:232385/140‑1 (MQ=255)
                                      ttattaAAATAAAGATATCCTACTTAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCAAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGa                                                                                               <  1:132610/140‑1 (MQ=255)
                                        atcacaaTAAAGATATCCTACATCATCTAATAAACATCCCAATAATTGAACGAATAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATTTTCAACATGTGCGTTGata                                                                                             <  2:242340/135‑1 (MQ=255)
                                        aTGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGata                                                                                             <  1:390130/140‑1 (MQ=255)
                                               gaaaGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTATTACAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATAttt                                                                                      <  2:264474/139‑1 (MQ=255)
                                                aaaGATTACCTACATAAACTAACACACATCCCAATAATAGAACGAGTAAAAAGCCAAAAATAAAAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtg                                                                                     <  2:447065/140‑1 (MQ=255)
                                                     tatCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATGGTCAATAAAAACAAAATCAGTAAAAATGATCAACATTTGCGTTGGAAGATATTggtgtat                                                                                >  1:345153/1‑138 (MQ=255)
                                                          tACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGGTGATAAATATTTGGTTGTCATGt                                                                           >  2:233307/1‑140 (MQ=255)
                                                          tACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATAAACATTTGCGTTGATATATATTTGTGTGTAATGt                                                                           >  2:470560/1‑140 (MQ=255)
                                                           aCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTTTTATTTTTTGTAGTAAAAATAGTCAATAATCATTAATACGGTCAAAATGCTCGACATTCGCGTTGACATATATTTGAGAGTcccgct                                                                          >  2:95249/1‑135 (MQ=255)
                                                           aCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTGTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTACTGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGtt                                                                          <  1:105905/140‑1 (MQ=255)
                                                              tAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  1:228842/140‑1 (MQ=255)
                                                              tAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  1:508388/140‑1 (MQ=255)
                                                              aaaaCTAAAAAGCATCCCAAAAATAGAAAGAGTAAAAAGCAAAAATAAAAAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  2:398648/139‑1 (MQ=255)
                                                               aaaCTAATACCTATCCCAATAATACAACGAGTAAACAGCAAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAAGGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcgc                                                                      <  2:449112/140‑1 (MQ=255)
                                                               aaaCTAATACACATCCAAATAATAGTACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCACTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcgc                                                                      <  1:332477/140‑1 (MQ=255)
                                                                        cacaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATTTACATGCGTTTGTCATGTTTCGCCGCCctttt                                                             >  2:524810/1‑138 (MQ=255)
                                                                        cacaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCt                                                             >  1:229206/1‑140 (MQ=255)
                                                                             ccaactaaaaGAACGAAGAAAACCCCAAATTCTTCAAAAAATATGTAGTAAAAATTGTCGATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGcc                                                        <  1:283669/135‑1 (MQ=255)
                                                                              ccAATAATAGAACAAGTTAAATGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCca                                                       <  2:272088/140‑1 (MQ=255)
                                                                                aataatAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca                                                     >  2:372549/1‑140 (MQ=255)
                                                                                aataatAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca                                                     <  1:120715/140‑1 (MQ=255)
                                                                                aaaaaaagaagtaGTAAAAAGCCAATTTTTTCAATAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca                                                     <  1:385008/128‑1 (MQ=255)
                                                                                  taataGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTATGTCATGTTTCGCCGCCTTTCTATACCCCAGc                                                   >  1:183982/1‑140 (MQ=255)
                                                                                       gAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCa                                              >  1:33599/1‑140 (MQ=255)
                                                                                               caaaaGCCAATACTTTCGACAAAGCGGTAGTAAAAATTGCCAATAATCATTAATGCAGTCAAAATGATCAACATTTGCTGTTATATATATGTGTGTGTCATGTTTCGCCGCCTTTCTATGCAACATCGGTCatatctttt                                      >  2:538574/2‑135 (MQ=255)
                                                                                               aaaaaGCCAATTTTTTCAAAGAATTTGTAGTAAAAATAGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCGACAGCCTTCATATAAttt                                      >  2:119925/1‑140 (MQ=255)
                                                                                                aaaaGCCAATATTTTTTTTAAAATTGAAGTAAAAATGGGCAATAATCATTAATCCAGTAAAAATGATCAACATTTGCGTTGTTATATATTTGTGTGTACTGTTTGGACGGTATGCTATTCTACAGCGTTCATATAATtta                                     >  2:113844/1‑140 (MQ=255)
                                                                                                    gCCAATTTTTTCAAAAAATATGTAATAAAAATTGTCAATAATCATAAATGCAGTAAAAATGATCAACATTTGCGTTGATATATAATTGTGTGGCGTGTTTCGCCGCCTTTCTATGCCAAATCGTTGATATAattaattaa                                 >  2:226908/1‑139 (MQ=255)
                                                                                                                                    ttGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCa  <  1:233307/140‑1 (MQ=255)
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ATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCA  >  CP000730/2028449‑2028719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: