Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,660 T→A 18.0% I173I (ATT→ATA)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6600TA18.0% 114.4 / 17.9 50I173I (ATT→ATA) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (17/24);  new base A (2/7);  total (19/31)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01

GGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110522‑110797
                                                                                                                                          |                                                                                                                                         
ggTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGAAGTAGATAttt                                                                                                                                          >  2:16936/1‑140 (MQ=255)
   tAAAATGGTCGATAATAAAATCACTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGAAATTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCat                                                                                                                                       >  2:393552/1‑140 (MQ=255)
     aaaTGATCGATAATAAAATCATTCCAACAAAAGAAAATAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                                     <  2:423165/140‑1 (MQ=255)
         tgtagATAATAAAATCATTCCAACAAAAGAAATGAAAGATGAAAATATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATc                                                                                                                                 <  2:379922/136‑1 (MQ=255)
             gATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCaga                                                                                                                             >  1:144387/1‑140 (MQ=255)
               taataaAATCCTTCAAACAAAAGAAATTAAAAATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAgg                                                                                                                           <  2:94431/140‑1 (MQ=255)
                 ataaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGTTg                                                                                                                         >  1:161205/1‑140 (MQ=255)
                   aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGcc                                                                                                                       <  1:31701/140‑1 (MQ=255)
                   aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATACAAATGTGca                                                                                                                       >  1:263412/1‑139 (MQ=255)
                    aaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGATATCGAAAACTTTAGGTTCTTTGTTTAATATGGCGACTTTAAAAATTTGTAAAATTATAAAGACGGAGATATTTCATATAATTCAGAGGTGCCg                                                                                                                      >  1:242319/1‑140 (MQ=17)
                     caccATTCAAGCAAAAGAATGTAAAGCTTAAAAAACAAAAAAATAAATCGTACACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                                     <  2:25575/137‑1 (MQ=17)
                     aaccATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                                     <  2:216950/137‑1 (MQ=255)
                     aaTCATTCCAACAAAAGAAATTAAAGATGAAAACATAAAAAATGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                                     <  1:150173/140‑1 (MQ=255)
                      aTCATTCCAACAAAAGAAATTAAAGATTAAAAAATAAAAAAAGATATCGAAAACTTTAAGTTCTTTGTGCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAg                                                                                                                    <  1:112742/140‑1 (MQ=255)
                       tCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                                   <  2:469290/140‑1 (MQ=255)
                                   aaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAAATTGAAAAATTATAAAGACGGAGATATTTCATATAAACCAGAGGTGCCGAGTTATTCGACTaaa                                                                                                       >  1:363744/1‑140 (MQ=255)
                                      aaaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGATAAatat                                                                                                    <  1:346368/140‑1 (MQ=255)
                                       aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACTGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                   <  2:127697/140‑1 (MQ=255)
                                       aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                   <  2:449757/140‑1 (MQ=255)
                                       aaTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATACGGCTAAATATc                                                                                                   >  2:436022/1‑140 (MQ=255)
                                         atAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                 <  1:450100/139‑1 (MQ=255)
                                          tAAAGATGAAAAAATAAAAAAAGAAATCGAAACCTTTAAGTTCTTTGTTCAATATGTCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAAGTGCCGAGTTATTCGACTAAATATGAAt                                                                                                >  1:209962/1‑140 (MQ=17)
                                          tAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAAt                                                                                                <  1:79130/140‑1 (MQ=255)
                                                  aaaaaaTAATAAAAGTAATCTTATATTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                        <  1:206600/140‑1 (MQ=17)
                                                  aaaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                        <  2:431445/140‑1 (MQ=255)
                                                   aaaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                       >  2:172749/1‑140 (MQ=255)
                                                     aaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTGAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGCGGGTCCGAGTTATTCGCGTGAATATCAATTAACTaagtag                                                                                     >  2:10505/1‑136 (MQ=17)
                                                       aTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCTAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                   <  1:377975/140‑1 (MQ=255)
                                                       aTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                   <  1:394410/140‑1 (MQ=255)
                                                          aaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAAACGGAGATATTTAATAAAATACAGAGGAGCCGAGTAATGCGGATAAAAAATAAATAACTAATGATAATta                                                                                >  1:425680/1‑140 (MQ=17)
                                                              aataaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAAt                                                                            <  2:402426/137‑1 (MQ=255)
                                                                                        gTTCAATATGGCGTCTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                                  <  1:194048/140‑1 (MQ=255)
                                                                                        gTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                                  <  1:311385/140‑1 (MQ=255)
                                                                                          tCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgata                                                <  2:539665/140‑1 (MQ=255)
                                                                                           cAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGAAAAACAATTACGCAAAAgatatgataa                                               >  1:47627/1‑139 (MQ=255)
                                                                                             atatGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAc                                             >  1:163979/1‑140 (MQ=255)
                                                                                                    taCTTTAAAAATTTTAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAg                                      <  2:395828/139‑1 (MQ=255)
                                                                                                       tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                                   <  1:395510/140‑1 (MQ=11)
                                                                                                        ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaaa                                  <  1:213132/140‑1 (MQ=11)
                                                                                                                   atgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                       <  2:455395/137‑1 (MQ=255)
                                                                                                                   atgaaTTATAAAGATGGAGATATATAATATAATCCAGAGGTGCCGAGTTATTCGTCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAACTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt                       <  2:231721/137‑1 (MQ=17)
                                                                                                                   aaaaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCACCAAAGtt                       >  1:271617/1‑140 (MQ=255)
                                                                                                                         tataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt                 <  2:433059/140‑1 (MQ=255)
                                                                                                                           taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa               <  1:338187/140‑1 (MQ=255)
                                                                                                                            aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATTAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAGAGTTATTGTTaaa              >  2:245862/1‑140 (MQ=255)
                                                                                                                              aGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAGATTATTGTTAAAAg            >  1:477068/1‑140 (MQ=255)
                                                                                                                              aGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTAGGCTAAATATCAATGAACTAATGATGATTATAATGTAAAAAAATTACGCAAAGAATATGATATACGGACGAATAAGGACTCAAAGTTATTGTTAAAAg            >  2:87273/1‑140 (MQ=17)
                                                                                                                                  ggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTc        <  2:435549/140‑1 (MQ=255)
                                                                                                                                    agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTACAg      >  1:448753/1‑140 (MQ=255)
                                                                                                                                    agaTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATAATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGGTATTGTTAAAAGGTTCAg      >  1:23586/1‑140 (MQ=255)
                                                                                                                                        atTTCATATAATCCATAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAACACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGaa  <  2:526169/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                         
GGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAA  >  USA300TCH1516_ALE/110522‑110797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑