Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,560 T→C 9.9% R210R (CGT→CGC)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5600TC 9.9% 121.5 / 6.3 51R210R (CGT→CGC) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (27/19);  new base C (3/2);  total (30/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.34e-01

AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACT  >  USA300TCH1516_ALE/111423‑111698
                                                                                                                                         |                                                                                                                                          
aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                                                                         <  1:476830/141‑1 (MQ=255)
  gTTTTTTGAGCAATATATTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                                                                                       <  2:407500/141‑1 (MQ=255)
   ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                                                                      <  1:45380/141‑1 (MQ=255)
    tttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGat                                                                                                                                     >  1:388307/1‑141 (MQ=255)
        tgggcAAGATAGCAATTTTAAGGATTTAATGAATTAGAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                                                                 <  2:468380/138‑1 (MQ=255)
        tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                                                                 >  2:273222/1‑141 (MQ=255)
           gcAATATAGCAATTTTAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatat                                                                                                                              <  1:132947/141‑1 (MQ=14)
           gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGatat                                                                                                                              >  1:213674/1‑138 (MQ=14)
                  agtaaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaaca                                                                                                                       <  2:375290/138‑1 (MQ=255)
                   gCAATTTTAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGGTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaacaa                                                                                                                      <  1:416692/141‑1 (MQ=255)
                      aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATa                                                                                                                   >  1:489610/1‑141 (MQ=255)
                        tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATAAAATACAGACATACCAATCTATTCAACTCAATATCAATTAACAAATGAACATTATAATATAAAACACTCAACTACCACATATAACATACCAACCAATaaa                                                                                                                 >  2:480414/1‑141 (MQ=255)
                         ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaaa                                                                                                                >  1:254202/1‑140 (MQ=255)
                         ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGATCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAAGTAAATTATATTAAATACCAAAAAATaaaa                                                                                                                >  2:324862/1‑140 (MQ=18)
                          tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAACATCGGCGTGTAAGTTAGGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                                                               >  1:235415/1‑141 (MQ=18)
                                    aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                                                                     <  1:59007/141‑1 (MQ=255)
                                       aagtataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                                                                  <  1:479993/138‑1 (MQ=255)
                                                  tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATGTAATTGAAAGGTAc                                                                                       >  2:53361/1‑141 (MQ=255)
                                                    ggaatatatCATATAATGCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                                                                     <  2:284489/138‑1 (MQ=255)
                                                     cgaTATAGCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACAAACGATGATTATAATGTAAAACAATTACGTAAAAGACAGGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                                                                    <  1:416102/140‑1 (MQ=17)
                                                      aatatatGATATAATACAGAGTTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACGAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                                                                   <  2:290388/140‑1 (MQ=255)
                                                        tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGaa                                                                                 >  1:77595/1‑141 (MQ=255)
                                                               tataATCCAGAGGTGACGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATATAGCGCCGAAGCTGGTGTTGAACGGTACAGGGAATTTaaaa                                                                          >  1:16710/1‑141 (MQ=255)
                                                                   aTCCAGAGGTGCCGAGTTATTAAGCTCAATAACAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAACAACAAATAAAGCGCGGAAGCTGTTGTTGAAAGGTACAGGAAATTAAAAAGGtt                                                                      >  2:97898/1‑141 (MQ=14)
                                                                       agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                                                                  <  2:49866/141‑1 (MQ=255)
                                                                        gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGATGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                                                                 >  2:97648/1‑141 (MQ=255)
                                                                         agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGAGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAACAGGTTCATCAg                                                                >  2:341514/1‑141 (MQ=255)
                                                                            tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACTAAACAAAAACGAGCCTACGCTGTTGTTGAAAGATACAGGGAATTACAAAGGTCCATCAGTTg                                                             >  2:105667/1‑141 (MQ=17)
                                                                             gCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAAAAAGACTCGTAGCAGATGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg                                                            >  2:299941/1‑141 (MQ=14)
                                                                                gAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAACGCTTCATCAGTTGGata                                                         >  2:246732/1‑141 (MQ=255)
                                                                                 aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat                                                        >  2:445560/1‑141 (MQ=255)
                                                                                        cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa                                                 >  2:10869/1‑141 (MQ=255)
                                                                                                             atgatgATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAgaga                            >  1:338566/1‑141 (MQ=255)
                                                                                                              tgatgaTTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGaa                           <  1:423185/141‑1 (MQ=255)
                                                                                                                 ttatggaaaTTTAAAACAACTACGTAAAATATAGGACATACCAACAAATAAAGCGCCGAATCTGTTGTTGAAAGGTACAGAGAATTTAAAATGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaa                        <  2:148684/134‑1 (MQ=17)
                                                                                                                 tgatTATAATGTAAAACAATTACGTAAAAGATATGAGGTACCAACAAATAAAGCTCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaa                        <  2:4629/141‑1 (MQ=255)
                                                                                                                  gatTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATaaa                       >  1:488507/1‑141 (MQ=255)
                                                                                                                       taATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAGATTGAATTTACTTTTTTAGAGAATAAAAATGa                  >  2:188336/1‑141 (MQ=255)
                                                                                                                       taATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGa                  >  1:164812/1‑141 (MQ=255)
                                                                                                                        aaTGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGGTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAACAAAAATGaa                 >  1:73115/1‑141 (MQ=255)
                                                                                                                        aaTGTAAAACAATTAAGTAAAAGGTATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaa                 <  2:78298/141‑1 (MQ=255)
                                                                                                                         aagTAAAAAAATGACGTAAAAGATATGACATAACAATAAATAAAGCGTCGAAGCTGTTGTTGAAAGGTACAGGGAATATAACAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGaaa                <  2:84164/139‑1 (MQ=18)
                                                                                                                             aaaaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAatat            <  1:43844/141‑1 (MQ=255)
                                                                                                                               aaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAatatat          >  2:276188/1‑139 (MQ=255)
                                                                                                                               aaCAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTACTCAAAGTTACACGGACTTTAAATCTTGCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAttt          <  1:471721/141‑1 (MQ=21)
                                                                                                                                  aaTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttact       >  1:99455/1‑141 (MQ=255)
                                                                                                                                   aTTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAAGTTCATCAGTTGGATATAAAAAAATTGAATCTACTTTTATAGAGAATAAAAATGAAAATAtttagtt      >  2:170959/1‑141 (MQ=255)
                                                                                                                                    ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTTAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt     >  2:288453/1‑141 (MQ=255)
                                                                                                                                    ttACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATAtttacttt     >  2:457148/1‑141 (MQ=255)
                                                                                                                                      aCGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACACGGAATTTAAAAGGTTCATCAGCTGGATATAAAAAAATTGAATTTACTTTTTTAGAGCATAAAAATGAAAATAtttactttac   >  2:194739/1‑141 (MQ=255)
                                                                                                                                       cGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATttactttact  <  1:356575/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                          
AAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGAATTTACTTTTTTAGAGAATAAAAATGAAAATATTTACTTTACT  >  USA300TCH1516_ALE/111423‑111698

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: ‑