Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,512 A→G 35.5% S194S (TCA→TCG)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG35.5% 47.9 / 45.5 52S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (15/18);  new base G (9/9);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 7.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAA  >  USA300TCH1516_ALE/111376‑111648
                                                                                                                                        |                                                                                                                                        
atGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                      <  2:86041/140‑1 (MQ=255)
   aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTGTTTTATAGCAATTCTAAAGATTTAATGAATTATAAATATCGAGATATATCATATAATTCAGCGGTGTCGCATTATTCTGCTCAat                                                                                                                                   >  2:330905/1‑141 (MQ=21)
   aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                   >  2:18728/1‑141 (MQ=255)
        gTTAAAGAAGAAAACATAAAGAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                                              <  2:155173/141‑1 (MQ=255)
          tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTAAAGAATTGGGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAtt                                                                                                                            >  1:309061/1‑141 (MQ=18)
           aacgaataaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTa                                                                                                                           <  1:181395/138‑1 (MQ=255)
           aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                                                           <  1:138678/141‑1 (MQ=255)
             agaagaAAACATAAAAAAAGAAATCGAAAACTGTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGTGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                         <  1:265045/141‑1 (MQ=255)
             agaagaAAACAAAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                         <  2:138512/141‑1 (MQ=255)
              gaagagAACATAAAAAAAGAAATCGCCACCTGCAAGTTTTATGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGCGTTATTCAGCTCAATATCAATTAACt                                                                                                                        >  1:290590/1‑141 (MQ=21)
                 gattaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAat                                                                                                                     <  2:55991/137‑1 (MQ=255)
                  aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatg                                                                                                                    <  1:328743/141‑1 (MQ=255)
                      cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCATCTCAATATCAATTAACTAAtgatga                                                                                                                >  1:329336/1‑141 (MQ=255)
                      cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAAtgatga                                                                                                                <  2:133974/141‑1 (MQ=255)
                        tAAAAAAAGAAATCGGAAACTTTAAATTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                              >  1:198534/1‑141 (MQ=255)
                        tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                              >  1:127706/1‑141 (MQ=255)
                         aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATta                                                                                                             <  2:311255/141‑1 (MQ=255)
                               aGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAAGGATGATTTTAATGt                                                                                                       <  1:211804/141‑1 (MQ=255)
                                     cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                 <  1:320071/141‑1 (MQ=255)
                                      gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACaa                                                                                                >  2:226860/1‑141 (MQ=255)
                                        aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                              >  1:66368/1‑141 (MQ=255)
                                         aaCTTTAAGTTTTTTGCTCAATATAGCAATTTTAAAGATTGAATGAATTATGAAGATGGGGATATATCATATAATCCAGAGGTGCCGAGTGATTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                             <  2:121902/141‑1 (MQ=17)
                                                    ttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGata                                                                                  <  1:389701/141‑1 (MQ=255)
                                                     tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                 >  1:308473/1‑141 (MQ=255)
                                                     tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                 <  2:211059/141‑1 (MQ=255)
                                                     tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGatat                                                                                 >  1:153243/1‑141 (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                                        <  1:153531/141‑1 (MQ=255)
                                                                                              aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                        <  1:59065/141‑1 (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)
                                                                                                                                        |                                                                                                                                        
CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAA  >  USA300TCH1516_ALE/111376‑111648

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: ‑