Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,651 C→T 10.9% D170D (GAC→GAT)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6510CT10.9% 131.4 / 5.9 53D170D (GAC→GAT) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base T (3/3);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

GATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTT  >  USA300TCH1516_ALE/110515‑110790
                                                                                                                                        |                                                                                                                                           
gATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                                          >  1:280198/1‑140 (MQ=255)
 atatCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgag                                                                                                                                         <  1:466743/140‑1 (MQ=255)
            aaaTGGTCGATAACAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                              <  1:162109/140‑1 (MQ=255)
               tGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAAt                                                                                                                           >  1:312833/1‑140 (MQ=255)
                ggTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATc                                                                                                                          >  2:440220/1‑140 (MQ=255)
                         taaAAACACTCCAATAAAAGAAATTAAATATGACAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCCACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGc                                                                                                                 <  1:112445/140‑1 (MQ=17)
                          aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGCCGGAGATATTTCATATAATCAAGAGGTGcc                                                                                                                >  2:164957/1‑140 (MQ=255)
                             aacATACCAACAAAAGAAAATAAAGAGGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                             <  2:413085/138‑1 (MQ=255)
                             aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                             <  1:198802/140‑1 (MQ=255)
                             aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                             >  1:378216/1‑140 (MQ=255)
                                  tCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCGGAGTTAtt                                                                                                        >  2:570729/1‑140 (MQ=255)
                                  tCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTATAAGTGCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAACGACGGAGATATTTCAAATAATAAAAAGTTGCTGAGatata                                                                                                        >  2:368917/1‑139 (MQ=17)
                                    caacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCg                                                                                                      <  1:241355/140‑1 (MQ=255)
                                     aacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                     >  2:267256/1‑140 (MQ=255)
                                      acaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAACATGATAAAAACGGAGATATTTCATATGATACAAAGATGACGATTAATTCGGc                                                                                                    >  2:338925/1‑140 (MQ=17)
                                      acaaAAGAAATTAAAGATGAAAAAAGAAAAAAAGAACGCGAAAAATCTAAGTTCTTTGTTCAATATGTCAACGGGAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGACGAGTTATTCGGc                                                                                                    >  2:232505/1‑140 (MQ=17)
                                         aaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTaa                                                                                                 >  1:262966/1‑140 (MQ=255)
                                            gAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                              >  2:562854/1‑140 (MQ=255)
                                             aaaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTACTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTCTTCGGATAAatat                                                                                             >  2:323650/1‑140 (MQ=255)
                                                   aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                       <  2:145230/140‑1 (MQ=255)
                                                   aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTa                                                                                       <  2:145233/140‑1 (MQ=255)
                                                        gAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTACTCGGCTAGATATCAATTAACTaa                                                                                  <  2:500357/140‑1 (MQ=255)
                                                         aaaaaaTAAAAAAAGAAATCGACAACTTTAAGTTCTTTGTTCAAAATGGCGCCTTGAGAAGTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                 <  1:540617/140‑1 (MQ=17)
                                                           aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                               >  1:336342/1‑140 (MQ=255)
                                                             aaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                             >  1:61097/1‑140 (MQ=255)
                                                              aTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAACTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                            >  1:157998/1‑140 (MQ=255)
                                                                  aaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                        <  1:173597/140‑1 (MQ=255)
                                                                      aGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                    <  2:413459/140‑1 (MQ=255)
                                                                            cGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTACCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAGTATAATGTAAAAc                                                              >  2:535037/1‑140 (MQ=255)
                                                                               aaaCTTTAAGTTCTTTGTTCAATATGGCTACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                           <  2:207190/140‑1 (MQ=255)
                                                                                 aCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                         >  1:273641/1‑140 (MQ=255)
                                                                                 aCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                         >  1:319823/1‑140 (MQ=255)
                                                                                 aCTTTAAGTTCTTTGTTCAATATGCGTACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGATGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                         <  2:493512/140‑1 (MQ=255)
                                                                                   tttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                       <  1:12979/140‑1 (MQ=255)
                                                                                    ttAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGc                                                      >  1:163708/1‑140 (MQ=255)
                                                                                      aaGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaa                                                    >  2:131141/1‑140 (MQ=255)
                                                                                       aGTTCTGTGAGCAATAGGGCGGCTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                   <  2:517410/140‑1 (MQ=18)
                                                                                                  cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatat                                        >  1:488890/1‑140 (MQ=255)
                                                                                                             cTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTa                             <  2:280198/140‑1 (MQ=255)
                                                                                                              tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                            <  1:5197/140‑1 (MQ=11)
                                                                                                              tttAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                         <  2:104453/127‑1 (MQ=255)
                                                                                                              tttAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                         >  1:104453/1‑127 (MQ=255)
                                                                                                                 aaaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGc                         <  1:309355/140‑1 (MQ=255)
                                                                                                                   aaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAAATATGATATACCGACGAGTAAAGCTc                       >  2:534486/1‑140 (MQ=255)
                                                                                                                    agtttGAAAAATTATAAAGACAGATATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTACCCAACGATCATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                      <  1:457237/138‑1 (MQ=18)
                                                                                                                    aaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                      <  1:292820/140‑1 (MQ=255)
                                                                                                                         gAAAAATGATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGt                 <  2:385046/140‑1 (MQ=255)
                                                                                                                          atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAACGCTCCACAgat                >  2:277324/4‑138 (MQ=14)
                                                                                                                           tgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa               >  1:566421/3‑140 (MQ=255)
                                                                                                                           ggaaTTATAAGGATGGAGATATATCATATAATCCAGAGGTGACGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAGTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa               <  2:22078/138‑1 (MQ=17)
                                                                                                                              aTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACAGACGAGTAAAGCTCCAGAGTTATTg            >  2:147859/1‑140 (MQ=17)
                                                                                                                               ttATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt           <  1:461522/140‑1 (MQ=255)
                                                                                                                                  taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa        <  1:92580/140‑1 (MQ=255)
                                                                                                                                        cGGAGATATTTCAGATAATCCAGTGATGCCGAGTTAGTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGtt  <  1:535619/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                           
GATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTT  >  USA300TCH1516_ALE/110515‑110790

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: ‑