Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,560 T→C 19.6% R210R (CGT→CGC)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5600TC19.6% 86.3 / 10.3 40R210R (CGT→CGC) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (17/15);  new base C (4/4);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTAC  >  USA300TCH1516_ALE/111428‑111697
                                                                                                                                    |                                                                                                                                         
ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGata                                                                                                                                   <  1:389701/141‑1 (MQ=255)
 tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                                                                  <  2:211059/141‑1 (MQ=255)
 tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                                                                  >  1:153243/1‑141 (MQ=255)
 tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                                                                  >  1:308473/1‑141 (MQ=255)
  ttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATg                                                                                                                                 >  1:98085/1‑141 (MQ=255)
     cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATgcta                                                                                                                              >  1:353329/1‑138 (MQ=255)
     cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGCGCCGAGTTATTCGGCTAAATATCAATTAACTAATGAGGATTATAATGTAAAACAATTACGCAAAAAATATGata                                                                                                                              >  2:302893/1‑139 (MQ=17)
        aaTATATCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGAGATGATATAc                                                                                                                           <  2:396122/141‑1 (MQ=14)
        aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAc                                                                                                                           <  1:27699/141‑1 (MQ=14)
        aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTACAACAATTACGTAAAAGATATGACATAc                                                                                                                           <  2:123015/141‑1 (MQ=255)
              gCAATTTTAAAGATTTAATGAGTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                     >  1:312310/1‑141 (MQ=255)
              gCAATTTTAAAGATTTAATGAATTAGAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                     >  2:167190/1‑141 (MQ=255)
                  ttttAAAGATTTAATGAATTAGAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaa                                                                                                                 <  2:363732/141‑1 (MQ=255)
                     tAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                                                              <  2:77517/141‑1 (MQ=255)
                     tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                                                              <  2:241779/141‑1 (MQ=255)
                              aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTCAACAATATGACATACCAATAAATAAATCGCCGAAGCt                                                                                                     >  2:271870/1‑141 (MQ=17)
                                 gAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgtt                                                                                                  <  1:250486/141‑1 (MQ=255)
                                          aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                                                                         <  1:59065/141‑1 (MQ=255)
                                          aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                                                                         <  1:153531/141‑1 (MQ=255)
                                                  atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGa                                                                                 >  2:26107/1‑141 (MQ=255)
                                                      atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                                                                             <  1:143851/141‑1 (MQ=255)
                                                              aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAATAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCGGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                                                                     <  2:243513/141‑1 (MQ=255)
                                                                ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTACAAGGTtca                                                                   >  1:130313/1‑141 (MQ=255)
                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                                                                >  1:377675/1‑141 (MQ=255)
                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcataa                                                                >  1:134053/1‑139 (MQ=255)
                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAAAGGGAATTTAAAAGGTtcatca                                                                >  1:273733/1‑141 (MQ=255)
                                                                     ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                                                              >  1:62665/1‑141 (MQ=255)
                                                                         ccGAGTGACTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAGCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGCACAGGGAATTTAAAAGGTTCGTCCGTTggg                                                          >  2:291129/1‑140 (MQ=14)
                                                                                aTTCATCACAATATCTATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAACCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa                                                   <  1:81724/141‑1 (MQ=255)
                                                                                aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaa                                                   >  1:303734/1‑141 (MQ=255)
                                                                                             tCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTAc                                      >  1:224005/1‑141 (MQ=255)
                                                                                              cAATTAAATAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAACGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACt                                     <  1:263381/141‑1 (MQ=255)
                                                                                                         tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                          <  1:154660/141‑1 (MQ=255)
                                                                                                            agatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaa                       <  2:382896/140‑1 (MQ=255)
                                                                                                             gatTATAATGTAAAACAATCACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTCAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaaa                      >  1:221576/1‑141 (MQ=255)
                                                                                                                    aTGTAAAACAATTACGTACAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGTAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaaa               <  2:329336/141‑1 (MQ=255)
                                                                                                                               ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt    >  2:328224/1‑141 (MQ=255)
                                                                                                                               ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt    >  2:349603/1‑141 (MQ=255)
                                                                                                                                tACGTAAAAGATATGACATACCAACAAATAAAGGGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttta   >  2:261180/1‑141 (MQ=255)
                                                                                                                                 aCGTAAAAGATATGACATACCAACAAATAAAGCGCCGTAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTTCTTTTTTAGAGAATAAAAATGAAAATAtttactttac  <  2:98085/141‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                         
TTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTAC  >  USA300TCH1516_ALE/111428‑111697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑