Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,660 T→A 10.5% I173I (ATT→ATA)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6600TA10.5% 152.1 / 8.3 56I173I (ATT→ATA) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (24/26);  new base A (3/3);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110527‑110796
                                                                                                                                     |                                                                                                                                        
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                                                                                                                   >  1:378216/1‑140 (MQ=255)
                 aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                                   <  1:198802/140‑1 (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                                                               >  1:319823/1‑140 (MQ=255)
                                                                     aCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                               >  1:273641/1‑140 (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)
                                                                                                                             ggAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTATTAAAAGGTTc       >  2:517423/1‑140 (MQ=255)
                                                                                                                                 atatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg   <  1:368917/140‑1 (MQ=255)
                                                                                                                                 atatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAggg   <  1:267256/140‑1 (MQ=255)
                                                                                                                                  tatTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGa  <  2:204583/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                        
AAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGA  >  USA300TCH1516_ALE/110527‑110796

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: ‑