Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,660 T→A 21.4% I173I (ATT→ATA)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6600TA21.4% 88.9 / 22.7 51I173I (ATT→ATA) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (12/28);  new base A (7/4);  total (19/32)
Fisher's exact test for biased strand distribution p-value = 7.54e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.83e-01

AATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCA  >  USA300TCH1516_ALE/110528‑110792
                                                                                                                                    |                                                                                                                                    
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                       <  1:587986/132‑1 (MQ=255)
                                                                                                              tgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                       <  2:353136/132‑1 (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)
                                                                                                                           tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTAGTATAATGTAAAACAATAACGCAAAAGATATGATATACAGACGAGTAAAGCTACAAAGTTATTGTTaa          >  2:295914/2‑134 (MQ=17)
                                                                                                                           tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTCCGCATTAGTTATAACATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa          >  2:587936/2‑134 (MQ=17)
                                                                                                                           tggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa          >  2:83609/2‑134 (MQ=255)
                                                                                                                               gaTATTGCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACTAGTAAAGCTCCAAAGTTATTGTTAAAAgg      <  2:42687/134‑1 (MQ=255)
                                                                                                                                   tttCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCa  >  1:150989/1‑134 (MQ=255)
                                                                                                                                    |                                                                                                                                    
AATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCA  >  USA300TCH1516_ALE/110528‑110792

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: ‑