Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,513,930 A→T 100% L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT100.0% 120.8 / NA 38L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (21/17);  total (21/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513796‑1514065
                                                                                                                                       |                                                                                                                                       
ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATCCTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTga                                                                                                                                    >  2:633412/1‑139 (MQ=255)
   tttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                 >  1:114732/1‑140 (MQ=255)
     tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACCAGCATCTATATCACTCATACTATGTTTTATCGTAtca                                                                                                                                >  1:142712/1‑138 (MQ=255)
               gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                     >  2:604413/1‑140 (MQ=255)
                cTTTATTATAAGCCATTGGCATGGGGTTTGCCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                    <  1:223460/140‑1 (MQ=255)
                cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                    <  1:636338/140‑1 (MQ=255)
                    attaGTAGCCATTGGCATGGTGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                <  1:446358/140‑1 (MQ=255)
                    attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                <  1:446586/140‑1 (MQ=255)
                       agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                             <  1:124101/140‑1 (MQ=255)
                          agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                          >  1:110476/1‑140 (MQ=255)
                            ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATTACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                        <  2:382348/140‑1 (MQ=255)
                               ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                                     >  1:495182/1‑140 (MQ=255)
                                tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                    >  1:613198/1‑140 (MQ=255)
                                 ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                   >  1:45471/1‑140 (MQ=255)
                                      ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                              >  1:578801/1‑140 (MQ=255)
                                             gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGt                                                                                       >  1:410727/1‑140 (MQ=255)
                                                  ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                  >  2:204255/1‑140 (MQ=255)
                                                     gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAATAGGATTATTAATGCCATTATTTGGATTATCACTTATGCTTGTATTtatag                                                                               >  1:375912/1‑139 (MQ=255)
                                                     gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCAGAATATGTTTTATTGTATTAGGATTATTAATGCCATTCTTTGGATTATCTCTTCTCCTTGTATTTATaa                                                                               >  1:386135/1‑140 (MQ=255)
                                                      aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTATATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                              <  1:533544/140‑1 (MQ=255)
                                                       tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAACAACCAGCTTCTAGATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAtt                                                                             <  1:143156/140‑1 (MQ=255)
                                                       tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAtt                                                                             <  1:536998/140‑1 (MQ=255)
                                                        aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATC‑‑TATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                          <  2:623297/140‑1 (MQ=255)
                                                         aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                           >  2:238539/1‑140 (MQ=255)
                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTCATGGCTAAATGGGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                 >  2:339653/1‑140 (MQ=255)
                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTCTTTATAATTGAATTAAtatta                                                                 >  1:648640/1‑140 (MQ=255)
                                                                    aaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACACATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                                >  1:176957/1‑140 (MQ=255)
                                                                          tGCAACAAAAGTACCACATCGCGT‑AAAAAGACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTACTGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                          <  1:290005/140‑1 (MQ=255)
                                                                           acAATAAAAGTATCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                         <  2:723307/139‑1 (MQ=255)
                                                                                   aGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCATTGAATTAATATTATATATTAAAGAtcgtc                                                 >  1:155381/1‑140 (MQ=255)
                                                                                   aGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAGGAtcgtc                                                 >  2:292849/1‑140 (MQ=255)
                                                                                          caTCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGCTTTATTGTATTAGGATTATTAATGCCTTTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                          <  1:390663/140‑1 (MQ=255)
                                                                                                          ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                           <  1:319183/140‑1 (MQ=255)
                                                                                                               aTCTATATCACTCATAATATGTTTTATTGTACTAAGATGATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                      <  1:516327/140‑1 (MQ=255)
                                                                                                                    tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCATTTAAAGTTTTGaa                 >  2:372319/1‑140 (MQ=255)
                                                                                                                         cTCATTATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc            <  1:392628/140‑1 (MQ=255)
                                                                                                                           cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa          <  2:110476/140‑1 (MQ=255)
                                                                                                                                   gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTata  >  1:502700/1‑138 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513796‑1514065

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: ‑