Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,560 T→C 11.3% R210R (CGT→CGC)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5600TC11.3% 146.5 / 8.7 56R210R (CGT→CGC) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (29/19);  new base C (2/4);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 3.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.44e-01

TTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTAC  >  USA300TCH1516_ALE/111421‑111697
                                                                                                                                           |                                                                                                                                         
ttAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCTAAGGTTTCCTAGTTATTCCGCTCAATAGCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                                                                           <  2:427589/140‑1 (MQ=18)
    gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                                                                       >  1:598950/1‑140 (MQ=255)
     ttttttGCGCAATATAGCAATTTTAAAGATATAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                                                                                      <  2:585392/140‑1 (MQ=255)
             gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                                                                              >  2:662650/1‑138 (MQ=255)
             gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACa                                                                                                                              <  2:139645/140‑1 (MQ=255)
                 tataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAcc                                                                                                                          <  1:196213/140‑1 (MQ=14)
                  atatCAATTGTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                                                                         <  1:217532/140‑2 (MQ=11)
                  ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                                                                         <  2:617668/140‑2 (MQ=14)
                  ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                                                                         <  1:51180/140‑2 (MQ=11)
                     gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                                                                                      >  1:605406/1‑139 (MQ=11)
                      cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATATAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                     >  2:279406/1‑140 (MQ=255)
                      cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTAAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGAAAAAGATATGAAATacaaacaa                                                                                                                     >  2:230072/1‑140 (MQ=18)
                          tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                                                                 <  1:232979/140‑1 (MQ=255)
                                gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                                                                           <  1:454233/140‑1 (MQ=255)
                                          aTTATAAAGATGGAGATATATCATAGAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                                                                 <  2:135832/140‑1 (MQ=255)
                                             ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttgttg                                                                                              >  1:646087/1‑140 (MQ=255)
                                              taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGa                                                                                             <  1:540590/140‑1 (MQ=255)
                                                 aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAg                                                                                          >  1:251440/1‑140 (MQ=255)
                                                  gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                                                                         >  2:357941/1‑140 (MQ=255)
                                                    tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTGAGCTCAATATCAATTAACTAATGATGATTATAATGTACAACAATGACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATGTTGTTGCAAggaa                                                                                       >  2:515793/1‑138 (MQ=14)
                                                     ggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAc                                                                                      <  1:540410/140‑1 (MQ=255)
                                                       agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                                                                    >  1:201782/1‑140 (MQ=255)
                                                         atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                                                                  <  2:580106/140‑1 (MQ=255)
                                                           atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAGTGGTGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                                                                >  2:650454/1‑140 (MQ=255)
                                                           atatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACCGAAACTGTTGTTGAAAGGTACAGCGaa                                                                                >  2:642189/1‑140 (MQ=255)
                                                                     aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                                                                      <  2:527428/140‑1 (MQ=255)
                                                                        cAGAGGTGCCGAGTTATTCAGCTCGATAACAAGTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                                                                   <  2:278378/140‑1 (MQ=255)
                                                                        cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtca                                                                   >  2:230873/1‑140 (MQ=255)
                                                                          gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                                                                 >  1:421169/1‑140 (MQ=255)
                                                                           agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                                                                >  1:405739/1‑140 (MQ=255)
                                                                             gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGGACAGGGAATTAAAAAGGTTCATCAGt                                                              >  1:598209/1‑140 (MQ=255)
                                                                               gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTGTTGAACGGTACAGGGAAATTAAAAGGTTCATCAGTTg                                                            >  2:691709/1‑140 (MQ=255)
                                                                               gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACAAACAAATAAAACGCCGAAGCTGTTGTTGAAAACGACCGGGAATATAAAAGGTTCATCAGtag                                                            >  2:309636/1‑138 (MQ=17)
                                                                                    gTTATTCAGCTCAAGATCAATTAACTAATGATGATTATAATGTAAAACAAGTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat                                                       <  2:300112/140‑1 (MQ=255)
                                                                                      tATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaa                                                     >  2:386057/1‑140 (MQ=255)
                                                                                      tATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACACGGAAGCTAAAAGGTTCATCAGTTGGATATaa                                                     >  2:643412/1‑140 (MQ=255)
                                                                                          cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaa                                                 >  1:490208/1‑140 (MQ=255)
                                                                                                aaTATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGaa                                           >  1:397064/1‑140 (MQ=255)
                                                                                                    tCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTa                                       >  1:540287/1‑140 (MQ=255)
                                                                                                    tCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTa                                       >  1:537486/1‑140 (MQ=255)
                                                                                                      aaTTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACt                                     >  1:609581/1‑140 (MQ=255)
                                                                                                          aaCTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACttttt                                 >  2:274955/1‑140 (MQ=255)
                                                                                                            cTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTAATTGTTTa                               >  2:200651/1‑140 (MQ=255)
                                                                                                             tAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTag                              <  1:310651/140‑1 (MQ=255)
                                                                                                               atgatgATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTagag                            >  2:260066/1‑140 (MQ=255)
                                                                                                                tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAgaga                           >  2:685989/1‑140 (MQ=255)
                                                                                                                 gatgatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                          <  1:343382/140‑1 (MQ=255)
                                                                                                                     atTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaaa                      <  1:249267/140‑1 (MQ=255)
                                                                                                                     atTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaaa                      <  2:201782/140‑1 (MQ=255)
                                                                                                                          aaTGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAAAAAACTTAATAAGAGAATAAAAATGa                 >  1:293042/1‑140 (MQ=17)
                                                                                                                           aTGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaa                >  2:518536/1‑140 (MQ=255)
                                                                                                                            tGTAAAACAATTACGTAAAAGATATGACATACCAACACAAAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaaa               <  1:190697/140‑1 (MQ=255)
                                                                                                                             gTAAAACAAATACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaaaa              <  2:133293/140‑1 (MQ=255)
                                                                                                                               aagaCAATTACTGAAAGTATATGACAGACCAACAAAGAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAATGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAata            <  2:422161/137‑1 (MQ=18)
                                                                                                                                 aaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtt          <  2:45077/140‑1 (MQ=255)
                                                                                                                                        aCGTAAAAGATATGACATACCAAAAAATATAGCGCCGAAGCTGTTGTTGAAAGGTACAGTGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttta   <  2:331668/140‑1 (MQ=255)
                                                                                                                                         cGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttactttac  >  1:240055/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                         
TTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTAC  >  USA300TCH1516_ALE/111421‑111697

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: ‑