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% 184.5 / NA 55L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (23/32);  total (23/32)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  USA300TCH1516_ALE/1513799‑1514064
                                                                                                                                   |                                                                                                                                      
tttGTATGTATCGCTTTATTATTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTa                                                                                                                               <  1:82351/141‑1 (MQ=255)
tttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATATTTTATTGTATTa                                                                                                                               >  2:796683/1‑141 (MQ=255)
              tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 <  1:23403/141‑1 (MQ=255)
              tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 <  2:141644/141‑1 (MQ=255)
              tttATTAGTAGCCATTGGCATGGGGTTTGGCTCGGGGATAACGAGTGCTCAAAAGACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 <  1:520960/141‑1 (MQ=255)
              ttgaagagtagACATGGGCAAGGTGTTTGACCCATGAATAAAGCGTAAAAAAAATACTCCAATAAAAGTAAAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 <  2:798906/135‑1 (MQ=255)
              gttaggagtagCCATTGGCAGGGGGTTTGCCTCTTGGAAAAAGGGTACAAAAAATACCGAAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                 <  2:654878/135‑1 (MQ=255)
               ttattaGTAGCCATTGGCATGGGGGTTGTCGCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGACTATTAATGCCa                                                                                                                >  2:456960/1‑141 (MQ=255)
                tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGGACCACATCGCGTAAAAAAACCAGCATCTATAGCCCTCATAATATGTATTATTGGATGAGGATTATTAATGCAat                                                                                                               >  2:492919/1‑141 (MQ=255)
                      tagCCATTGGTATGGGGTGTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAGTAGGATTATTAATGCCATTATTTg                                                                                                         <  1:91513/141‑1 (MQ=255)
                              ggcagtgggTTTGTCTCTTAGAAAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCAGCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 <  1:143767/135‑1 (MQ=255)
                              ggCATGGGGTTGGTCTCTTGGATAAAGCGTTCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 <  1:629421/141‑1 (MQ=255)
                                gaTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAATAGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                               <  2:541421/140‑1 (MQ=255)
                                cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                               <  2:584519/141‑1 (MQ=255)
                                 aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAACATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTTTGAGGATTATTAATGCCATTATTTGAATTAttaatt                                                                                              >  1:294768/1‑136 (MQ=255)
                                 aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                              >  2:683648/1‑141 (MQ=255)
                                    gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                           >  1:946166/1‑141 (MQ=255)
                                       tttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCtt                                                                                        >  2:684606/1‑141 (MQ=255)
                                       tttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCtt                                                                                        <  1:319784/141‑1 (MQ=255)
                                          ttctcTTGGATAAAGCGTAGAAAAAATACTGCAATAAAATTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                     <  2:761110/140‑1 (MQ=255)
                                            ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                   >  2:889826/1‑141 (MQ=255)
                                            ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                   >  1:939751/1‑141 (MQ=255)
                                              ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                 <  1:922666/141‑1 (MQ=255)
                                                  taTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                             <  1:457809/140‑1 (MQ=255)
                                                  gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                             <  2:914389/141‑1 (MQ=255)
                                                     aatgCGTACAAAAAATACTGCAATAAAAGGAACACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                          <  2:149451/138‑1 (MQ=255)
                                                     aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                          <  1:831443/141‑1 (MQ=255)
                                                      aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATAACTCATAATATGTTTTATTGTATTAGGATTATTAATGAAATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                         >  2:694798/1‑141 (MQ=255)
                                                       aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        >  2:583609/1‑141 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAGCCAGCATCTATATCCCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTCTAATTGAAtt                                                                       >  2:6466/1‑141 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCCCTTATCCTTGTATTTATAATTGAAtt                                                                       >  2:264913/1‑141 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAttt                                                                       >  2:215058/1‑141 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                       >  2:215666/1‑141 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                       <  1:864135/141‑1 (MQ=255)
                                                        gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTCGTATTTATAATTGGAtt                                                                       >  2:739774/1‑141 (MQ=255)
                                                                      cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                         <  1:557570/141‑1 (MQ=255)
                                                                      cTGCAATAAAAGTACCACATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                         <  1:910137/141‑1 (MQ=255)
                                                                       tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                        <  2:46045/141‑1 (MQ=255)
                                                                           aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTAATAATATGTTCTGTTGAATGAGCATAATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCATTGAATTAATATTATATATTAAAGaa                                                    >  2:396331/1‑140 (MQ=255)
                                                                             aaaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcg                                                  <  1:109769/141‑1 (MQ=255)
                                                                             aaaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcg                                                  <  1:992578/141‑1 (MQ=255)
                                                                                        atagtgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTATGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                       <  2:324672/136‑1 (MQ=255)
                                                                                        atagcgTACAAAAACGAGCATCTATATCTCTCATATTCTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                       <  2:856582/138‑1 (MQ=255)
                                                                                                 aaaaaCCAGCATCTATTTCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  2:1049581/141‑1 (MQ=255)
                                                                                                 aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  2:159715/141‑1 (MQ=255)
                                                                                                 aaaaaCCAGCATCTATATACCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  2:10349/141‑1 (MQ=255)
                                                                                                  aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACCATAATGCAc                             >  2:241219/1‑141 (MQ=255)
                                                                                                     aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                          >  2:84352/1‑141 (MQ=255)
                                                                                                     aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATCAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAACATCGTCGTGCTAAACAATCATGCACTTa                          >  2:768120/1‑141 (MQ=255)
                                                                                                      ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                         <  2:747886/141‑1 (MQ=255)
                                                                                                               atatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGaa                >  2:1090514/1‑141 (MQ=255)
                                                                                                                    ccTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc           <  2:999480/140‑1 (MQ=255)
                                                                                                                    aCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc           <  1:578679/141‑1 (MQ=255)
                                                                                                                         taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt      >  2:991361/1‑141 (MQ=255)
                                                                                                                             atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  >  1:680814/1‑141 (MQ=255)
                                                                                                                                   |                                                                                                                                      
TTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  USA300TCH1516_ALE/1513799‑1514064

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: ‑