Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,190,716 A→G 7.6% Y128H (TAT→CAT)  USA300HOU_RS11190 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,190,7160AG 7.6% 137.6 / 3.2 58Y128H (TAT→CAT) USA300HOU_RS11190hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (32/19);  new base G (2/2);  total (36/22)
Fisher's exact test for biased strand distribution p-value = 6.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.48e-01

TACACCAATTCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGTTTTTCAAATG  >  USA300TCH1516_ALE/2190579‑2190856
                                                                                                                                         |                                                                                                                                            
tACACCAATTCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATGAAg                                                                                                                                           >  1:471282/1‑141 (MQ=255)
tACACCAATTCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATGAAg                                                                                                                                           >  1:471283/1‑141 (MQ=255)
tACACCAATTCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAg                                                                                                                                           >  1:513112/1‑141 (MQ=255)
       ttttcATGTTTCATTTATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGTGTCaaa                                                                                                                                    <  2:16441/137‑1 (MQ=255)
       aatCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCaaa                                                                                                                                    <  1:23558/139‑1 (MQ=255)
        ttCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACTTGCTTCACTTCTATCTATTATTTCATTTTCGTCTTGAGCACCCGCTGTATAAAGGGTCAAAg                                                                                                                                   >  1:543173/1‑141 (MQ=255)
          ccATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGACTCTCGGTATGGTACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTTAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGtt                                                                                                                                 >  1:612298/1‑141 (MQ=255)
            aTGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACTTGATTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTAACAAGTGTCAAAGTTGc                                                                                                                               >  2:304244/1‑141 (MQ=255)
            aTGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTTAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGc                                                                                                                               >  2:315619/1‑141 (MQ=255)
              gTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTTCTTCACTTCTATCTATTAATTCATTTTCAGCTTGACCACCCGCTGATAAAAGGGTCAACGTTGCtt                                                                                                                             >  2:422532/1‑140 (MQ=255)
              gTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAACGGGTCAAAGTTGCTa                                                                                                                             >  2:47722/1‑141 (MQ=255)
                 tCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTTAATCTACGTGCTTCACTTCTATTTATTAATTCAATTTCAGCTTGACTACCCCATGTATTAAGAGTCAAAGTTGTTACTc                                                                                                                          >  2:649054/1‑141 (MQ=255)
                 tCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAACGAGTCACAGTTGCTAATc                                                                                                                          >  2:41989/1‑141 (MQ=255)
                   aTTGATTAGTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAGCCATCGTGTCAATCTACGTGCTTCATTTCTTTCTATTAATTCAATTTCAGCTTGCCCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGa                                                                                                                        <  2:237205/141‑1 (MQ=255)
                    ttGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGAt                                                                                                                       >  1:730747/1‑141 (MQ=255)
                          attCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACTCGCTGTATAAAGGGCCAAAGTTGCTAATCGATAGCGtc                                                                                                                 <  2:236484/141‑1 (MQ=255)
                            tCCTCATTTTTATTGTTTTCTAACTGTCTCTCTTTCTTTAACCTTCGTTTCAATCTATATGCTTCACTTCTATCTATTAATTCAATTTCATCTTGACCACCCGCTGTATAAAGGGTCCATGTTGCTAATCATTAGCGtttg                                                                                                               >  2:701302/1‑138 (MQ=255)
                            tCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACTACCCGCTGTATAACGGATCAAAGTTACTCATCTATAGCGtctc                                                                                                               >  2:249838/1‑141 (MQ=255)
                             ccTCTTTTTTTTTGTTTTCTTATTGTGTTTTGTTATTTATTCATTGTTTGAATCTACGTGCTTCACTTCTATTTATTAATTCAATTTCAGTTTGACCTCTCTCTGTATAAAGGGTCAAAGTTACTAATTGTTAGCGTCTCa                                                                                                              <  2:17757/141‑1 (MQ=255)
                                 aTTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATtat                                                                                                          >  1:71665/1‑141 (MQ=255)
                                    tttATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTTTCATTATAgg                                                                                                       >  1:455700/1‑141 (MQ=255)
                                      tATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGAc                                                                                                     >  2:712065/1‑141 (MQ=255)
                                        ttGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCa                                                                                                   <  1:765498/141‑1 (MQ=255)
                                          gTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATGAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAAc                                                                                                 <  2:471282/141‑1 (MQ=255)
                                          gTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATGAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAAc                                                                                                 <  2:471283/141‑1 (MQ=255)
                                                 aaaTGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGata                                                                                          >  2:484764/1‑141 (MQ=255)
                                                  aaTGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGatat                                                                                         <  1:710935/141‑1 (MQ=255)
                                                  aaTGTCTCTCGGTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGatat                                                                                         <  2:528487/141‑1 (MQ=255)
                                                    tGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCTGTATCa                                                                                       >  1:173931/1‑141 (MQ=255)
                                                            gTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTg                                                                               >  1:121972/1‑141 (MQ=255)
                                                            gTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTg                                                                               >  1:242205/1‑141 (MQ=255)
                                                              tATTTAACCATGGTGTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCAGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCAGTATAGGACCAACATCGATATCAATATTTTGaa                                                                             <  2:688534/141‑1 (MQ=255)
                                                              tATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGaa                                                                             >  2:75706/1‑141 (MQ=255)
                                                                 ttAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATAc                                                                          >  1:780324/1‑141 (MQ=255)
                                                                    aCCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGaa                                                                       >  1:710182/1‑141 (MQ=255)
                                                                      cATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGaaaa                                                                     <  2:513112/141‑1 (MQ=255)
                                                                         cgcttCAATCTAGGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTCTAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGCTCTCAATATTTTGAATACGAAAatat                                                                  >  2:736204/4‑141 (MQ=255)
                                                                            ttCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGt                                                               >  2:183522/1‑141 (MQ=255)
                                                                             tCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAATGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTa                                                              >  1:320697/1‑141 (MQ=255)
                                                                             tCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTa                                                              >  1:139920/1‑141 (MQ=255)
                                                                                 tCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTAc                                                          <  2:71665/141‑1 (MQ=255)
                                                                                             aCTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGGATACGAAAATATGGTATTACCTTTTCATCCaa                                              >  1:255826/1‑141 (MQ=255)
                                                                                                   atctatTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTCCCTTTTCATCCAaaaataa                                        >  2:295217/1‑141 (MQ=255)
                                                                                                     ttatTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAaaaataaaa                                      <  1:41989/140‑1 (MQ=255)
                                                                                                     ctatTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAaaaataaaa                                      <  2:780324/141‑1 (MQ=255)
                                                                                                     ctatTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACAAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAaaaataaaa                                      <  2:455700/141‑1 (MQ=255)
                                                                                                      tatTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAaaaataaaat                                     >  1:328852/1‑141 (MQ=255)
                                                                                                        ttAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGc                                   >  1:352448/1‑141 (MQ=255)
                                                                                                                    cAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTacac                       >  1:73571/1‑141 (MQ=255)
                                                                                                                     tgCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACg                      <  1:584328/140‑1 (MQ=255)
                                                                                                                      ggctGACCAGCGGTTATATTAAGAGTAAAAGTTGTTATTCGCTAGCGGCTGATTATAGGTCATTCATTTATATGATTTTGTTTAATACGAAAATATGGTTTTACAATTCCAATCATAAATAAAATGCCGTTTCGTACACGc                     <  2:55406/138‑1 (MQ=255)
                                                                                                                         tGACCACACGCAGTATAAAAGGTCAAAGTTGATAATAGATAGCGTCTAATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCaaa                  <  2:142068/141‑1 (MQ=255)
                                                                                                                           accgccCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATg                <  2:337093/141‑1 (MQ=255)
                                                                                                                           accaccCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTCGCGTACAACCAAATg                >  2:20191/1‑141 (MQ=255)
                                                                                                                                 ctatGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGAACAACATCGATATCAATAGTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGttt          <  2:23120/138‑1 (MQ=255)
                                                                                                                                  gCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGtttt         <  1:632911/141‑1 (MQ=255)
                                                                                                                                   cTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATGTTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGttttt        >  1:77038/1‑141 (MQ=255)
                                                                                                                                     gTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATACCGTTTCGTACACGCAAATGGTGTTTTTCa      >  1:721959/1‑141 (MQ=255)
                                                                                                                                         aaaGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGTTTTTCAAATg  >  2:528904/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                            
TACACCAATTCCATGTATCATTGATTATTCCTCATTTTTATTGTTTTCTAAATGTCTCTCGTTATTTAACCATCGTTTCAATCTACGTGCTTCACTTCTATCTATTAATTCAATTTCAGCTTGACCACCCGCTGTATAAAGGGTCAAAGTTGCTAATCGATAGCGTCTCATTATAGGACCAACATCGATATCAATATTTTGAATACGAAAATATGGTATTACCTTTTCATCCAAAAATAAAATGCCGTTTCGTACACGCAAATGGTGTTTTTCAAATG  >  USA300TCH1516_ALE/2190579‑2190856

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: ‑