Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,028,622 G→T 32.7% T8K (ACG→AAG)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,6220GT32.7% 62.6 / 34.5 56T8K (ACG→AAG) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (19/17);  new base T (9/9);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

AATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTT  >  USA300TCH1516_ALE/2028494‑2028750
                                                                                                                                |                                                                                                                                
aaTAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGat                                                                                                                             <  1:122690/134‑1 (MQ=255)
  aaaaGAAATACTACATAAACTAATACACAACCAAACACTAGAACAAATAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATCAATGCAGTAAAAATGATCAACATTTGCGTTGatat                                                                                                                           <  1:136849/133‑1 (MQ=255)
     atatatCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGatatata                                                                                                                        <  1:109085/132‑1 (MQ=255)
     aGATATCCTACATAAACTAATACATATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGatatata                                                                                                                        <  2:182741/134‑1 (MQ=255)
      gATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTCATGCAGTAAAAATGATCAACAATTGCTTTGatatatat                                                                                                                       >  2:230910/1‑134 (MQ=255)
      gATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGatatatat                                                                                                                       >  1:190853/1‑134 (MQ=255)
       atatCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTATTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATAtt                                                                                                                      <  1:532445/134‑1 (MQ=255)
         atCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtg                                                                                                                    <  1:407728/134‑1 (MQ=255)
          tCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTAATATATACTtga                                                                                                                   >  2:75504/1‑133 (MQ=255)
             tACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATAAATTtgagtg                                                                                                                >  2:574994/1‑134 (MQ=255)
                            acaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCgccgcc                                                                                                 >  1:162613/1‑134 (MQ=255)
                            acaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCgccgcc                                                                                                 <  2:603692/134‑1 (MQ=255)
                             caTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGAAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCt                                                                                                >  2:411798/1‑134 (MQ=255)
                              aTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCtt                                                                                               >  1:71632/1‑134 (MQ=255)
                                 ccAATAATAGAACGAGTAAAACGCCAATCGTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGTGTTGATATATATTTGTGTGTCATGTTTCGCCGCCtttat                                                                                            >  2:73430/1‑132 (MQ=255)
                                 ccAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCt                                                                                            >  1:531395/1‑134 (MQ=255)
                                     taataGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAAACATGAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGc                                                                                        <  1:195154/134‑1 (MQ=255)
                                          gAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCCGTAAAAACGAACAACATTTGAATAGAGATAAATTTGTGTGTCAAGTTTAGCCACCATTCTATGCCACAg                                                                                   >  1:226966/1‑134 (MQ=255)
                                              gAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGtt                                                                               <  2:196370/134‑1 (MQ=255)
                                                 tAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTTGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCat                                                                            <  1:302419/134‑1 (MQ=255)
                                                   aaaaGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCatat                                                                          >  2:499425/1‑134 (MQ=255)
                                                   aaaaGCCAATTTTTTCAAAAAATATGTAGTAAAAAATGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTCGatat                                                                          >  2:74149/1‑134 (MQ=255)
                                                    aaaGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTGATGTTTCGCCGCCTTTCTATGCCACAGCGTTCAtata                                                                         <  2:562118/134‑1 (MQ=255)
                                                    aaaGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCAtata                                                                         >  2:523600/1‑134 (MQ=255)
                                                     aaGCCATTTTTTTCAAAAAATATTTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATaa                                                                        <  1:453870/134‑1 (MQ=255)
                                                           aTTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCAGATAATttagt                                                                  >  1:91307/1‑132 (MQ=255)
                                                               tttCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTGGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGAt                                                              <  1:486570/134‑1 (MQ=255)
                                                                   aaaaaaTATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCCCAGCGTTCATATAATTTATTAGATACGa                                                          >  1:559272/1‑134 (MQ=255)
                                                                    aaaaaTGTGTAGTAACAATGTGCAATAATCATTAATGCAGTAACAATGATCTACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCTTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGAt                                                         <  2:272664/134‑1 (MQ=255)
                                                                       aaTATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATggt                                                      >  2:109824/1‑132 (MQ=255)
                                                                        atatGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATTAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGttt                                                     <  1:540806/134‑1 (MQ=255)
                                                                        atatGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTACATACGATGttt                                                     <  2:531395/134‑1 (MQ=255)
                                                                          atGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATAAGATGtttgt                                                   >  2:124450/1‑132 (MQ=255)
                                                                                  aaaaTTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGc                                           <  2:71632/134‑1 (MQ=255)
                                                                                         gtaataagAATTAATGCAGTAAAAATGATCAACCTTTGCGTTAATATATATTTGTGTGTGATGTTTCGCCGCATTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTAttttt                                    <  2:20241/132‑1 (MQ=255)
                                                                                         gCAATAACCATTAATTCAGTATAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTCatttt                                    <  2:533654/134‑1 (MQ=255)
                                                                                              aatCATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGt                               >  1:447738/1‑134 (MQ=255)
                                                                                              aatCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGt                               >  1:494402/1‑134 (MQ=255)
                                                                                              aatCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAACGATCACCATATCTACTACAAACGATGTTTTTTCTGTTGCTATTTTTTCAGt                               >  1:600112/1‑134 (MQ=255)
                                                                                              aatCATGAATGCAGTAAAGATGATCACCAGTTGCTTTGATATATATTTGTTTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGt                               <  2:396534/134‑1 (MQ=255)
                                                                                                 cATTAATGCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCACTTATATGGAGCGGGGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGa                            >  1:282416/1‑134 (MQ=255)
                                                                                                 cATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGa                            >  1:112551/1‑134 (MQ=255)
                                                                                                  aTTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGac                           >  2:516066/1‑133 (MQ=255)
                                                                                                      aTGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGttt                       >  1:494976/1‑134 (MQ=255)
                                                                                                        gCAGTAAAAATGATCAACTTTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTttgt                     <  2:25377/134‑1 (MQ=255)
                                                                                                        gCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTttgt                     <  1:109824/134‑1 (MQ=255)
                                                                                                        gCAGTAAAAATGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCACCGCCTTTCTATGCCACAGCGTTCATATCATTTATTAGATACGATGTTTTTTATGTTGCTATTTTTTCAGTTGACGttttt                     >  2:248834/1‑132 (MQ=255)
                                                                                                        gCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTttgt                     >  2:325123/1‑134 (MQ=255)
                                                                                                           gTAAAAATGATGACCTTTTGCCTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGa                  <  2:361124/134‑1 (MQ=255)
                                                                                                              aaaaTGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGTGGCCTTTCTATACAACAGCCTTCTTGTACTTTATTAGATACGATGTTGTTTCTGTTACGATTTTTTCACTTGCGGTttgttgtgtt               >  2:64412/1‑130 (MQ=255)
                                                                                                                aaTTATCAACATTTTTGTTGATTTATATTTTTGTGTCAAGTGTCGCCGCCTTTCTAGGCCACAGCGTTCATATAAATTATTAGATACGATGTTTTTTCTGTTGCTATGTTTTCAGTTGAAGTTTGTTGAATTTg             <  1:75504/134‑1 (MQ=255)
                                                                                                                  tGATCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGTTGTTTTTTCTGTTTCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAg           >  1:238165/1‑134 (MQ=255)
                                                                                                                   gATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt          <  1:523600/134‑1 (MQ=255)
                                                                                                                    aTCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGtt         <  1:499425/134‑1 (MQ=255)
                                                                                                                     tCAACATTTGCTTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGttt        <  1:431904/134‑1 (MQ=255)
                                                                                                                           tttGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTGTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGTTATTTTTTTAGTTGAAGTTTGTTGAATTTGAGTTTGAAttt  >  1:353102/1‑134 (MQ=255)
                                                                                                                                |                                                                                                                                
AATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTT  >  USA300TCH1516_ALE/2028494‑2028750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑