Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 642,696 T→A 36.5% Q219H (CAA→CAT)  yjjP_1 ← Inner membrane protein YjjP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE642,6960TA36.5% 33.8 / 38.8 41Q219H (CAA→CAT) yjjP_1Inner membrane protein YjjP
Reads supporting (aligned to +/- strand):  ref base T (16/10);  new base A (8/7);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 7.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

TTTAAGATCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATAACGGCGATAATCCCAATAACTAATGAACCAATGAAT  >  USA300TCH1516_ALE/642559‑642831
                                                                                                                                         |                                                                                                                                       
tttAAGATCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTg                                                                                                                                       >  1:327726/1‑140 (MQ=255)
 ttAAGATCCAAAACATAGTCTAATCCTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTCACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGt                                                                                                                                      <  2:47318/140‑1 (MQ=255)
   aaGATCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTAt                                                                                                                                    <  1:314845/140‑1 (MQ=255)
    aGATCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTAtt                                                                                                                                   <  1:149639/140‑1 (MQ=255)
      aTCCAAATCATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGc                                                                                                                                 <  1:68095/140‑1 (MQ=255)
      aTCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAAAAAATCTTGTATTGc                                                                                                                                 >  1:61802/1‑140 (MQ=255)
            aaCATAGTCTGATACGCCTATACTAAAATTAATACGCGACCAACGCCAGCACGGATGCCAAACGCAGTAACCAATGCTTCGAATGATGTCGGTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGt                                                                                                                           >  2:89644/1‑140 (MQ=255)
             aCATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTCCGTTTGtt                                                                                                                          >  2:165863/1‑140 (MQ=255)
                tAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTTttatt                                                                                                                       >  1:98059/1‑140 (MQ=255)
                     tGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATac                                                                                                                  <  1:180528/140‑1 (MQ=255)
                        tACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAAAGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTTTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACAcc                                                                                                               >  2:184132/1‑140 (MQ=255)
                         aCTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCa                                                                                                              <  1:356263/140‑1 (MQ=255)
                            ccTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAgaa                                                                                                           >  2:36659/1‑138 (MQ=255)
                                    aaaaTTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAgg                                                                                                   >  2:241569/1‑140 (MQ=255)
                                             aCGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGc                                                                                          >  1:73131/1‑140 (MQ=255)
                                               gCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCg                                                                                        >  2:31624/1‑140 (MQ=255)
                                                    cAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATg                                                                                   >  1:210089/1‑140 (MQ=255)
                                                    cAACGCCAGCACCGATGCCAAACACGGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCACTg                                                                                   >  1:172688/1‑140 (MQ=255)
                                                      aCGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAACCTTCTATTGCGTTTGTTATTAATACACAAGGAACAATAGGCATGACTGACGCgatgat                                                                                 >  1:63627/1‑140 (MQ=255)
                                                       cGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGata                                                                                >  1:50031/1‑140 (MQ=255)
                                                           aGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAg                                                                            <  2:56045/140‑1 (MQ=255)
                                                           aGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAg                                                                            <  2:231372/140‑1 (MQ=255)
                                                             cACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGtt                                                                          >  1:62831/1‑140 (MQ=255)
                                                                    gCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGt                                                                   <  2:21336/140‑1 (MQ=255)
                                                                         aCGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCt                                                              >  2:282263/1‑140 (MQ=255)
                                                                         aCGCAATAACCAATGCTTCTAATGATTGCGTTGTGAACATAAACACTAGTCCACCAACTAAATCTTGTATTACGTTTGTCATTAATACACCAGGAACACTCGGAATGACTGCCGCAATGATAATAGTTGCAAAGTCAcgt                                                              >  2:172336/1‑138 (MQ=255)
                                                                          cGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTg                                                             <  1:53186/140‑1 (MQ=255)
                                                                              gTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCCATGATAATAGTTGCCAAGTCACCTGTTgg                                                         >  2:84843/1‑140 (MQ=255)
                                                                               tAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGa                                                        <  2:207936/140‑1 (MQ=255)
                                                                                aaCCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGaa                                                       <  1:30324/140‑1 (MQ=255)
                                                                                         ttCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAATTCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTAt                                              <  2:188197/140‑1 (MQ=255)
                                                                                               tGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCaa                                        <  1:107074/140‑1 (MQ=255)
                                                                                                      gTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAGCAATAGGCATGACTGCCGCAATGATAATTGTTGTCAAGTCACTTGTTGGAATAAGTGTGTGTCCAATAACGGc                                 >  1:22644/1‑140 (MQ=255)
                                                                                                      gTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGGATAAGTGTATGTCCAATAACGGc                                 <  2:122815/140‑1 (MQ=255)
                                                                                                       ttGTGAAAACCAGCATGCGCTCACCAAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATAACGGCg                                <  2:156148/140‑1 (MQ=255)
                                                                                                             aaaTCAACATGTGTCCACCAAATAAATCTTGTATGTCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATAACGGCGATAATc                          <  1:59615/138‑1 (MQ=255)
                                                                                                                    cATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATAACGGCGATAATCCCAATaa                   >  1:120407/1‑140 (MQ=255)
                                                                                                                     aTGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTAGCCAAGGCACCTGTTGGAATAAGTGTATGTCCAATAACGGCGATAATCCCAGTAAc                  >  1:350089/1‑140 (MQ=255)
                                                                                                                           ccaccaAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCTATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATCACGGCGATAATCCCAAAAACTAAGGa            >  2:206378/1‑140 (MQ=255)
                                                                                                                              ccaAATAAATCATGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCAGCACTGACGCAATGAGAGTAGATGCCAAATCACGTGTTGGAGAAAGTCTAGGTCCAATAACGGCGATAATCCCAATAACTACTGAAcc         >  2:89452/1‑140 (MQ=255)
                                                                                                                                     aatCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAAAAAGTGTATGTCCAATAACGACGATAATCCCAATAACATATTAACACATGAAt  >  1:114443/1‑140 (MQ=255)
                                                                                                                                         |                                                                                                                                       
TTTAAGATCCAAAACATAGTCTGATACTCCTATACTAAAATTAATACGCTACCAACGCCAGCACCGATGCCAAACGCAGTAACCAATGCTTCTAATGATTTCGTTGTGAACATCAACATGTGTCCACCAAATAAATCTTGTATTGCGTTTGTTATTAATACACCAGGAACAATAGGCATGACTGCCGCAATGATAATAGTTGCCAAGTCACCTGTTGGAATAAGTGTATGTCCAATAACGGCGATAATCCCAATAACTAATGAACCAATGAAT  >  USA300TCH1516_ALE/642559‑642831

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: ‑