Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,651 C→T 14.5% D170D (GAC→GAT)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6510CT14.5% 108.6 / 10.8 54D170D (GAC→GAT) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (14/30);  new base T (4/4);  total (20/34)
Fisher's exact test for biased strand distribution p-value = 4.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.32e-01

ATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATT  >  USA300TCH1516_ALE/110518‑110779
                                                                                                                                     |                                                                                                                                
atCCGTTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGAc                                                                                                                                  <  1:403462/134‑1 (MQ=255)
   cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAACACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                               >  2:300339/1‑134 (MQ=255)
   cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAGATTATAAAGACGga                                                                                                                               >  2:306152/1‑134 (MQ=255)
   cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                               >  1:438033/1‑134 (MQ=255)
   cGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTATGTTCAACATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                               >  1:343405/1‑134 (MQ=255)
    ggTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgag                                                                                                                              <  1:74612/134‑1 (MQ=255)
     ggtAAAATGGTCGATAATAAAATCATTCACCTCTACTTAATAAAAGAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgaga                                                                                                                             <  2:427319/132‑1 (MQ=18)
          aaTAGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACATGAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATAttt                                                                                                                        <  1:15359/134‑1 (MQ=255)
            gagTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCa                                                                                                                      <  2:275639/132‑1 (MQ=255)
               tCGATAATAAAAACATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                   <  2:549851/134‑1 (MQ=255)
                    aataaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATcc                                                                                                              <  1:463650/134‑1 (MQ=255)
                     ataaAATCAATCCAAAAAAAGAAATTAAAGAAGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCa                                                                                                             <  2:231129/134‑1 (MQ=255)
                               tCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAACATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCAGa                                                                                                   >  1:42687/1‑134 (MQ=255)
                                      aaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGAAGGAGATATTACATATAATCAAGAGGTGCTGATTTATTc                                                                                            >  1:499598/1‑134 (MQ=17)
                                        aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAATTTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATGGGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                          <  1:157318/134‑1 (MQ=255)
                                        aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGACAGTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                          <  2:495243/134‑1 (MQ=255)
                                           aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTAAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCAAGTTATTCGGcaa                                                                                       >  2:56088/1‑132 (MQ=255)
                                           aaTTAAAGATGAAAAAATAAAAAAAGAAAACGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                       <  1:125570/134‑1 (MQ=255)
                                                 aGATGAAAAAATAAAAAAAGATAACGAAATCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                 <  2:550259/134‑1 (MQ=255)
                                                      aaaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTAGGCTAAATATCAATTa                                                                            >  1:192062/1‑134 (MQ=255)
                                                        acaaaaaaaaaaGAAATCTAAAACTTTAAGTTCTTTGTTCAATATAGTGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                          <  2:242288/129‑1 (MQ=14)
                                                        aaaaaaaaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                          <  2:334655/134‑1 (MQ=255)
                                                         aaaTAAAAAAATTAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                         <  2:506287/134‑1 (MQ=255)
                                                         aaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                         <  1:76903/134‑1 (MQ=255)
                                                                aaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                  <  1:21319/134‑1 (MQ=255)
                                                                aaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                  <  1:167207/134‑1 (MQ=255)
                                                                     ataTCGAAAACGTTAAGTTCTTTTTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                             <  2:181247/132‑1 (MQ=255)
                                                                       aTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                           >  2:538517/1‑134 (MQ=255)
                                                                         cGAAAACTTTTAGTTCTTTGTTCAATAGGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                         <  2:446763/134‑1 (MQ=255)
                                                                           aaaaCTGTAAGTTCTTTGTTCAATGTGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                       <  2:124373/134‑1 (MQ=255)
                                                                                  tAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATGCAGAGGTGCCGCGTTATTCGGCTAAATATCAATTAACTACTGATGATTATAATGTAAAACAAt                                                >  2:6373/1‑134 (MQ=255)
                                                                                  tAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                >  2:384220/1‑134 (MQ=255)
                                                                                     gTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                             <  1:447320/134‑1 (MQ=255)
                                                                                        atttGTTCAATATGACGACTTTAAAAATTTGAAAAATTAAAAAGACGGAGAGATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCa                                          <  1:398152/133‑1 (MQ=255)
                                                                                         tttGTTCAATATTGCGATTTTAAAAATTAAAAAAATTATAAAGACAGTACTATTTCAAATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACCAATGATGATTATAATGTAAAACAATTACGCaa                                         <  1:203364/134‑1 (MQ=17)
                                                                                         tttGTTCAATATGGCGACTTTAAAAATTCGAGTAAGTTGACAGACGGATATAGTTCATATAATCCAGAGGTGCCGAGTTATTCTGCTATATATAAATTAACTAATGATGATTATAATGTACAACAATTatgaaa                                         >  2:130970/1‑129 (MQ=14)
                                                                                         tttGTTAAATATGACAACTTTAAAAAATTGAAAAATAACAAAAACGGAGAAAGTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATTTAAAACAATTACGCaa                                         <  1:397466/134‑1 (MQ=17)
                                                                                                    tGGTGACATTAAAAATTAGAAAAATTATAAAGACGGAGATATTTCATATACTCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                              <  1:118822/134‑1 (MQ=255)
                                                                                                      tcGACTTTAAAAATTAGAAAAATTATAAAGACGGAGATATTTCATATAATCAAGAGGTGCAGAGTTATGCGGCTAAATATCAATTAACGAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                            <  1:45092/133‑1 (MQ=18)
                                                                                                      gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGAtata                            >  2:437112/1‑134 (MQ=255)
                                                                                                      gCGACTTTAAAAATTTGAAAAATTATAAAGAAGGAGATATTTCATATAATACAGAAGTATCGAGTTATTAGGCTAAATATAAATTAACTAATGTAGATTTTAATGTAAAAGAATTAAGCCAAAAATATTAaata                            >  2:505020/1‑134 (MQ=255)
                                                                                                               aaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATAATATACCGACGAGt                   >  2:447483/1‑134 (MQ=255)
                                                                                                                 aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCTGAGGTGCCAAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                 <  1:540253/134‑1 (MQ=255)
                                                                                                                  aTTTGAAAAATTATAAAAACGGAGATATTTCATATAATCCAGAGGTGCAGAGTTATTCGGCTAAATATCAATTAACTAGTGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaga                >  2:598640/1‑132 (MQ=255)
                                                                                                                   gttGAAAAATTATAAAGACGGAGATATTTCATATAAGCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAg               <  1:409495/133‑1 (MQ=255)
                                                                                                                    ttaattaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGc              <  1:70621/128‑1 (MQ=255)
                                                                                                                       aaaaaTTATAAAGACGGATATATTGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc           <  2:79859/134‑1 (MQ=255)
                                                                                                                       aaaaaTTAAAAAGACGGGGATATTTCATATAAGCCAAAGTTGCCGAGTTATTCGGCTAATTTTGGCTTGGCGAAGCATGATTATTATTTAAAAGAAGTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc           <  1:604886/134‑1 (MQ=16)
                                                                                                                        tgaaTTATAAAGATGGAGATATATTATATAATCCAGAGGTGCCAAGATCCTCTGCTAAATATCAATTAACTAATGATGATTATAACGTAAAATAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa          <  2:242328/132‑1 (MQ=14)
                                                                                                                        tgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa          <  2:353136/132‑1 (MQ=255)
                                                                                                                        tgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa          <  1:587986/132‑1 (MQ=255)
                                                                                                                            ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGt      >  2:43544/1‑134 (MQ=255)
                                                                                                                             tataAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTCGGCTAAATATCAATTCACTAATGATGATTATAATGTAAAACAATTAGTCAAAAGATATGATATAGCGACGCATCAAGCTCCAAAGtt     >  2:22328/1‑134 (MQ=14)
                                                                                                                                aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTCtt  >  1:315079/1‑134 (MQ=255)
                                                                                                                                aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt  >  1:163345/1‑134 (MQ=255)
                                                                                                                                     |                                                                                                                                
ATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATT  >  USA300TCH1516_ALE/110518‑110779

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑