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% 107.3 / NA 33L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (12/21);  total (12/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACG  >  USA300TCH1516_ALE/1513794‑1514056
                                                                                                                                        |                                                                                                                              
atttatttTTATGTATAGAGTAATAAATAGACAGACGCAACGCGTTAGTCTCAAAGATAAAGCGTACAAAAAAAACTCCAATAAAAGTACAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTg                                                                                                                            <  2:99871/141‑1 (MQ=255)
  ttatttTTATGTATCTCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATACTATGTTTTATTGTa                                                                                                                          <  2:381415/141‑1 (MQ=255)
       tgtatgtaTCGCTTTAGTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                     <  1:314464/141‑1 (MQ=255)
           tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATAGTATTAGGatta                                                                                                                 <  1:290377/141‑1 (MQ=255)
                  cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATACAAGTACCACATCGCGTAAAAAAACCAGCATCAATATCACTCATAATATGATATATTCTATTAGGATTATTAATGc                                                                                                          >  2:196729/1‑141 (MQ=255)
                  cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATCTCACTCATACTATGTTTTATTGTATTAGGATTATTAAttc                                                                                                          >  1:150545/1‑139 (MQ=255)
                   tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTTCCACATCGCGTAAGAAAACCAGCATCTATATCGCTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                         <  2:326114/141‑1 (MQ=255)
                     tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTCTTATATTAGGATTATTCATGGCat                                                                                                       >  2:316770/1‑141 (MQ=255)
                         agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                   <  1:256720/141‑1 (MQ=255)
                           tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTAGATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                 >  2:384241/1‑141 (MQ=255)
                             gCCATTCGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACAGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAtttttt                                                                                               <  2:189671/141‑4 (MQ=255)
                                  tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAAGAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGAATTATc                                                                                          >  2:421811/1‑141 (MQ=255)
                                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATTCTATTATTTGGATGATCa                                                                                         >  2:277179/1‑141 (MQ=255)
                                       tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                     >  1:531181/1‑141 (MQ=255)
                                                          aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGGATTAGGATTATTAATGCCATGATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                  <  1:137877/141‑1 (MQ=255)
                                                           aaGCGAACAAAAAATACGTCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                 <  2:164569/141‑1 (MQ=255)
                                                            aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                <  2:504133/141‑1 (MQ=255)
                                                             gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                               <  1:260394/141‑1 (MQ=255)
                                                             acGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                               <  1:416205/140‑1 (MQ=255)
                                                              ggTAAAAAAAAGACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCGCTTTCCCTTTGATTTATAATTGAATTa                                                              <  2:542738/140‑1 (MQ=255)
                                                                    aaaacTACCGCAAGAACATTACCGCATGTCGTCAAACAATCGGAATGTATGTGACTCTGAATATGTTTTATTGTAGTAGGATTACTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                        <  2:197032/141‑1 (MQ=255)
                                                                    aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCATTGTATTTATAATTGAATTAAtatta                                                        <  2:349218/141‑1 (MQ=255)
                                                                       aaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatat                                                     >  2:301113/1‑141 (MQ=255)
                                                                           cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCAGTATTTGGATTATCACTTATCCCTGTATTTATAATTGAATCAATATTATATATTa                                                 <  1:293556/141‑1 (MQ=255)
                                                                              cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATttattataa                                              >  2:445006/1‑138 (MQ=255)
                                                                               aaTAAAAGTACCACATCGCGTAAAAACACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                             <  1:423274/141‑1 (MQ=255)
                                                                               aaTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCCCTTATCCTTGTATTTATAATTGTATTTATATTATATATTAAAGa                                             <  2:51051/141‑1 (MQ=255)
                                                                                                  gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                          >  1:560733/1‑141 (MQ=255)
                                                                                                   tAAAAAAACCAGCACCTATATCACTCATAACATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATCATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGACCATCGAGCTAAACaataat                         >  1:387969/1‑141 (MQ=255)
                                                                                                      aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                      <  2:531181/141‑1 (MQ=255)
                                                                                                           ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                 <  1:277179/141‑1 (MQ=255)
                                                                                                                     tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAATTAAAGTTTTGAAc       >  1:232111/1‑141 (MQ=255)
                                                                                                                          cTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACg  <  1:375595/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                              
ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACG  >  USA300TCH1516_ALE/1513794‑1514056

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: ‑