Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,796,110 A→G 8.1% S86S (TCA→TCG)  USA300HOU_RS14370 → N‑acetylmuramoyl‑L‑alanine amidase domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,796,1100AG 8.1% 173.4 / 2.2 63S86S (TCA→TCG) USA300HOU_RS14370N‑acetylmuramoyl‑L‑alanine amidase domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base A (31/25);  new base G (2/3);  total (34/29)
Fisher's exact test for biased strand distribution p-value = 6.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

TCTCATGATTCAAAAAAATCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTCGGATA  >  USA300TCH1516_ALE/2795970‑2796249
                                                                                                                                            |                                                                                                                                           
tctcATGATTCAAAAAAATCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCa                                                                                                                                             <  1:76715/141‑1 (MQ=255)
 ctcATGATTCAAAAAAATCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAg                                                                                                                                            <  1:131508/141‑1 (MQ=255)
           aaaaaaaTCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACaa                                                                                                                                  >  2:278298/1‑141 (MQ=255)
           aaaaaaaTCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGAAAAAAATAATACAAGTAACCAAGAAAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAAACTAAAACaa                                                                                                                                  >  2:59341/1‑141 (MQ=255)
                 aTCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCAt                                                                                                                            <  2:210607/141‑1 (MQ=255)
                     aaTGACGATTGAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCGCTTCAGACTCTAACAATATCATTggt                                                                                                                        >  1:488654/1‑139 (MQ=255)
                     aaTGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGAt                                                                                                                        >  1:195148/1‑141 (MQ=255)
                      aTGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGAtt                                                                                                                       >  2:26996/1‑141 (MQ=255)
                       agACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGAttt                                                                                                                      <  1:59763/140‑1 (MQ=255)
                             tGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATAAAAGTAACCAAGACAATAAAGACAGAAAATTTAAAACTATAGACGACAGCACTTCCAACTCTAACAATATCATTTGTtttattta                                                                                                                >  2:72214/1‑141 (MQ=255)
                              gAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTttatttat                                                                                                               >  1:176325/1‑141 (MQ=255)
                              gAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTttatttat                                                                                                               <  1:610530/141‑1 (MQ=255)
                                     cTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAAtt                                                                                                        >  2:406105/1‑141 (MQ=255)
                                     cTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAAtt                                                                                                        >  2:272106/1‑141 (MQ=255)
                                               aacAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATATATAAGAATTTACCACAAAc                                                                                              <  1:132191/140‑1 (MQ=255)
                                                acAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAAcc                                                                                             <  1:262497/141‑1 (MQ=255)
                                                acAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAAcc                                                                                             >  1:270655/1‑141 (MQ=255)
                                                     tAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCGGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAatat                                                                                        >  2:338718/1‑141 (MQ=255)
                                                     tAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCGGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAatat                                                                                        >  2:9127/1‑141 (MQ=255)
                                                       aaGATATTGATAACGCAGACAACAATAACACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATaa                                                                                      <  2:458088/141‑1 (MQ=255)
                                                        aGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAAAAATATCATTGATTTTATTTATAAGAATTGACCACAAACCAATATaaa                                                                                     >  2:336977/1‑141 (MQ=255)
                                                         gATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTCCAGACTCTAACAATATCATTGATTTTATTCATAAGAATTTACCACAAACTAATATAAAc                                                                                    >  2:88688/1‑141 (MQ=255)
                                                             ttGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAAt                                                                                >  2:657959/1‑141 (MQ=255)
                                                              tGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAAtt                                                                               >  2:447938/1‑141 (MQ=255)
                                                                aTAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACATGAACAATATGATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGc                                                                             <  1:289141/141‑1 (MQ=255)
                                                                 tAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCt                                                                            >  2:550964/1‑141 (MQ=255)
                                                                 aaaaGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCt                                                                            <  1:557587/140‑1 (MQ=255)
                                                                     gCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCt                                                                            <  1:584901/137‑1 (MQ=255)
                                                                     gCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCt                                                                            >  2:584901/1‑137 (MQ=255)
                                                                         aCAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCaaaa                                                                    >  1:539047/1‑141 (MQ=255)
                                                                         aCAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACAaaaa                                                                    >  1:493203/1‑141 (MQ=255)
                                                                          cAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCaaaaa                                                                   >  1:500345/1‑141 (MQ=255)
                                                                           aaaaaTAACACAAGTAACCAAGACAAAAACGACAAAAAATTTCACACTTTACCCTACAGCACTTTGGTCTCTTACATTCTCAATGTTTATAATTAGAATAATTTACCACAACCCAATATATACCAATTGCTAACCAAaaat                                                                  <  2:239555/141‑1 (MQ=255)
                                                                               ataataCAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCCATATAACCCAATTGCTACCCAAaaataaaa                                                              >  1:62242/1‑140 (MQ=255)
                                                                               ataataCAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAaaataaat                                                              >  2:564032/1‑141 (MQ=255)
                                                                                taataCCAGTAACCAAGACAATATCGACAAAAAATTTAATACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAaataaata                                                             <  2:165938/141‑1 (MQ=255)
                                                                                taataCAAGTAACCAAGACAATAACGACAAAACATTTAATACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCTATTGCTAAGCAAAaataaata                                                             <  1:345349/141‑1 (MQ=255)
                                                                                taataCAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAaataaata                                                             <  1:444178/141‑1 (MQ=255)
                                                                                    aCAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACgat                                                         >  2:47538/1‑141 (MQ=255)
                                                                                      aaGCAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACgatga                                                       <  2:549724/141‑1 (MQ=255)
                                                                                       aGTAACCAAGACAATAACGACAAAAAATTTAAAACTATCGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAAGAAATACgatgat                                                      >  1:61003/1‑141 (MQ=255)
                                                                                           aCCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAAtt                                                  >  2:489242/1‑141 (MQ=255)
                                                                                              aaGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAACTAAATACGGGGATAATTACt                                               >  1:249386/1‑141 (MQ=255)
                                                                                              aaGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACt                                               <  1:420210/141‑1 (MQ=255)
                                                                                              aaGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACt                                               <  2:484765/141‑1 (MQ=255)
                                                                                               aGACCATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTc                                              <  2:644997/141‑1 (MQ=255)
                                                                                                 aCAATAACGACAAAAAATTTAAAACGATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCAt                                            >  1:294517/1‑141 (MQ=255)
                                                                                                     aaaCGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAAGCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTaac                                        <  1:442360/140‑1 (MQ=255)
                                                                                                      aaCGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTaaaa                                       >  1:587964/1‑139 (MQ=255)
                                                                                                                aaTTTAAAACTATAGACGACAGCACTTGAGACTCTAACAATATCATTGATTTTATTTATAAGAGTTTGCTTCAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATcc                             >  2:388328/1‑141 (MQ=255)
                                                                                                                 aTTTAAAACTATAGACGACAGCACTTCTGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACTAATTGCTAACCAAAAATACATACGATGATAATTACTCATTAACAACTTGAATCCa                            <  2:419266/141‑1 (MQ=255)
                                                                                                                     aaaaCTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAAc                        <  2:534078/141‑1 (MQ=255)
                                                                                                                     aaaaCTATACCCGCCAGCACTTCAGACTCTAACAATATCATTGATTTTACTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCACAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAAc                        <  1:104516/141‑1 (MQ=255)
                                                                                                                         cTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTAt                    <  1:278298/141‑1 (MQ=255)
                                                                                                                           ataGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAGCTTTAATCCAAAACTTATTc                  >  1:492476/1‑141 (MQ=255)
                                                                                                                           ataGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTc                  >  1:28960/1‑141 (MQ=255)
                                                                                                                             aaacgacAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCaa                <  2:542384/139‑1 (MQ=255)
                                                                                                                                     gCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCTAAACTTATTCAATTTAAAtt        <  1:406105/141‑1 (MQ=255)
                                                                                                                                     gCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAAtt        <  1:272106/141‑1 (MQ=255)
                                                                                                                                      cACTTCGGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTc       <  1:338718/141‑1 (MQ=255)
                                                                                                                                      cACTTCGGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTc       <  1:9127/141‑1 (MQ=255)
                                                                                                                                      cACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTc       >  1:598024/1‑141 (MQ=255)
                                                                                                                                        cTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTCgg     >  1:29675/1‑141 (MQ=255)
                                                                                                                                           cAGACTCTAACAATATCATTGATATTATTTATAAGAATTTACCACAAACCAATATAAACCAAATACAAACAAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTCGGata  <  2:488654/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                           
TCTCATGATTCAAAAAAATCTAATGACGATGAAACTTCTAAGGATACTACAAGTAAAGATATTGATAAAGCAGACAAAAATAATACAAGTAACCAAGACAATAACGACAAAAAATTTAAAACTATAGACGACAGCACTTCAGACTCTAACAATATCATTGATTTTATTTATAAGAATTTACCACAAACCAATATAAACCAATTGCTAACCAAAAATAAATACGATGATAATTACTCATTAACAACTTTAATCCAAAACTTATTCAATTTAAATTCGGATA  >  USA300TCH1516_ALE/2795970‑2796249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑