Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 195,286 T→A 21.4% intergenic (‑97/‑82) USA300HOU_RS00900 ← / → USA300HOU_RS00905 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE195,2860TA21.4% 121.1 / 30.9 56intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (31/13);  new base A (5/7);  total (36/20)
Fisher's exact test for biased strand distribution p-value = 9.18e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

TCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAGA  >  USA300TCH1516_ALE/195154‑195423
                                                                                                                                    |                                                                                                                                         
tCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCAATATATATGTTTATTTACTTATACCCTAACATGGTTTTTATACTCTTTGGAGATCTTTTTTACGGAATTTTATCTTAATTTTTaaaaaaaa                                                                                                                                   >  1:31222/1‑140 (MQ=255)
     cTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCtt                                                                                                                              <  2:519955/141‑1 (MQ=255)
      tAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTTTTTACTTATACCCTAACATGATTTTTATACTATTTGAAAATATATTTTACAGAATTTTATTTAAATATTTAAAAAAATATCTTa                                                                                                                             >  2:60327/1‑141 (MQ=255)
      tAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATTTTa                                                                                                                             >  2:349152/1‑141 (MQ=255)
          cTTGCTAAGATAGAATCTTTATCCATAATGATAGCCACCTATATAAATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCAAAAAAAAAAAAAAAATATCTTAatat                                                                                                                         <  2:499925/141‑1 (MQ=255)
            tGCTACGACCAATTCTTTCTCCATAATGATAGCCTCTTAGATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGACTTTTATCTAAATATTTAAAAAAATATCTTAATATcc                                                                                                                       <  2:188188/141‑1 (MQ=255)
             gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCt                                                                                                                      >  2:512312/1‑141 (MQ=255)
              cTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCtt                                                                                                                     >  2:508968/1‑141 (MQ=255)
                         tCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATAATCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATa                                                                                                          <  2:481939/141‑1 (MQ=255)
                          cTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTCAATATTTAAAAAAATATCTTAATATCATTGTAATCCGATaa                                                                                                         >  1:107671/1‑141 (MQ=255)
                             tATCCATAATTATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGaa                                                                                                      <  2:509412/141‑1 (MQ=255)
                             tATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGaa                                                                                                      >  2:538694/1‑141 (MQ=255)
                                ccATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTGTCTAGATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATta                                                                                                   >  1:536124/1‑141 (MQ=255)
                                   tAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAg                                                                                                >  1:404001/1‑141 (MQ=255)
                                          atcccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtt                                                                                         <  1:350516/139‑1 (MQ=255)
                                          aGCCCCCTATATCAATGTTTATTTACTTCTACTCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtt                                                                                         <  1:582945/141‑1 (MQ=255)
                                          aGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTTTTTTAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTATAATCCGATAAGAATTATAGTattatt                                                                                         >  2:6751/1‑141 (MQ=255)
                                                 tatatctcTGTTTTTGTACTTGAATCATAAGATGATTTTTTAAATATTTGAAAATATATTTTACTTATTTTTATCAAAAAAAATAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                                  <  2:106001/141‑1 (MQ=255)
                                                    atatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGTTAAGAATTATAGTAATATTTTTTCAACCa                                                                               >  1:345434/1‑141 (MQ=255)
                                                     tatatTTTTAGTGACTTATACCCTAACATGAATTTTATACTCTTTGAAAATATAGTTTACAGAATGTTATAAAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAt                                                                              <  2:259552/141‑1 (MQ=255)
                                                       tatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTg                                                                            <  1:182441/141‑1 (MQ=255)
                                                           tttagttaCTTATACCCTAATATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                        <  2:258584/141‑1 (MQ=255)
                                                              atttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagg                                                                     <  1:81965/141‑1 (MQ=255)
                                                              atttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagg                                                                     <  1:82149/141‑1 (MQ=255)
                                                              atttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTAGAGTAATATTTTTTAAACCAGTGTTATagg                                                                     >  1:353919/1‑141 (MQ=255)
                                                               tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagga                                                                    <  1:302666/141‑1 (MQ=255)
                                                                 taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATaggagg                                                                  >  2:328940/1‑141 (MQ=255)
                                                                 taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAACTATAGTAATATTTTTTCAACCATTGTTATaggaga                                                                  >  2:519021/1‑140 (MQ=255)
                                                                  aCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGt                                                                 <  1:508968/141‑1 (MQ=255)
                                                                   cttacgcccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTc                                                                <  1:74817/135‑1 (MQ=255)
                                                                   cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGCATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGtt                                                                >  2:447529/1‑140 (MQ=255)
                                                                   cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAAGATTAAAAAAAATATCTTAATATCCTTGTAATCCGCTAAGAATTATAGTAATATTTTTTCAACAATTGTTATAGGAGGTc                                                                >  2:186191/1‑141 (MQ=255)
                                                                    ttATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt                                                               >  1:189421/1‑141 (MQ=255)
                                                                    ttATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt                                                               >  1:521780/1‑141 (MQ=255)
                                                                      ataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtta                                                             >  1:567225/1‑141 (MQ=255)
                                                                         cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCAATAAGAATTATAGTAATATTTTTTCAACCATTGTTGTAAGACGACttatta                                                          >  2:501923/1‑141 (MQ=255)
                                                                            tAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATg                                                       <  2:225057/141‑1 (MQ=255)
                                                                             aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTATTATTAATGa                                                      >  1:586083/1‑141 (MQ=255)
                                                                              aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGACTTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc                                                     >  2:46029/1‑141 (MQ=255)
                                                                              aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc                                                     <  1:223094/141‑1 (MQ=255)
                                                                              aCATGATTTTTATACACCTTGAAAATAAACTTTACAGAATTTTATCTAAATAATTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc                                                     <  2:20911/141‑1 (MQ=255)
                                                                                aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTTTACTTTTTTTATAGGAAGTCTTATTAATgcaat                                                   >  2:33153/1‑137 (MQ=255)
                                                                                   aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACattat                                                >  1:196303/1‑141 (MQ=255)
                                                                                    tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGACTTATAGTAATATTTTTTAAACCATTGTTATAGGAGGTCTTATTAATGACattatt                                               >  2:277330/1‑141 (MQ=255)
                                                                                    tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCTTCTTTTGTTATATGAAATCTTATTAATGACattatt                                               >  2:399830/1‑141 (MQ=255)
                                                                                    tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACattatt                                               <  1:105105/141‑1 (MQ=255)
                                                                                           ttttttttAAAATAAAAGTTACAGAATTTTATTTAAATATTTAAAAAAATATCTTAATATCCTTGTCATCCGATAAGAATTATTTTAATATTTTTTCAACCATTGTTATAGGAGTTCTTATTAATGACATTATTTttattt                                        >  2:461382/5‑140 (MQ=255)
                                                                                                ttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGc                                   >  1:302888/1‑141 (MQ=255)
                                                                                                     aaTATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACa                              >  2:415168/1‑141 (MQ=255)
                                                                                                      atatatTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                             >  2:229447/1‑141 (MQ=255)
                                                                                                        atatTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCACCCATTGTTATAGGAGGGCTTATTAATGACATTATTTTTATTAGAAGCTAACAATc                           >  1:552558/1‑141 (MQ=255)
                                                                                                        atatTTTACAGAATTTTATCTAAATAATTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGACTTATAGTAATATTTTTTAAACAATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGATGCTAACAATc                           >  2:414875/1‑141 (MQ=255)
                                                                                                         tatTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCt                          >  2:162375/1‑141 (MQ=255)
                                                                                                            tttACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGa                       >  2:499503/1‑141 (MQ=255)
                                                                                                                    aTTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTCTTATAGAATGTCTTTTTAATGACATTATTTTTATTAGAAGTCAAACATCTGGATTTTGAAt               >  2:228736/1‑141 (MQ=255)
                                                                                                                                 atTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAagaaga  >  1:12604/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                         
TCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAGA  >  USA300TCH1516_ALE/195154‑195423

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: ‑