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% 140.3 / NA 42L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (22/20);  total (22/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513793‑1514066
                                                                                                                                         |                                                                                                                                        
aaTTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAtt                                                                                                                                       >  1:11366/1‑141 (MQ=255)
aaTTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAtt                                                                                                                                       >  1:606932/1‑141 (MQ=255)
     tattttatgtagCGTCTTACTAGTATCCATGGGCATGGGGTTTGTCTCTTGGATAAATCGTACAAAAAATACTGCAATAAAAGTACCACTTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                  <  2:193007/136‑1 (MQ=255)
          tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                             >  1:448711/1‑141 (MQ=255)
          tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                             >  1:354322/1‑141 (MQ=255)
                 cGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATGCTGCAATAAAAGTACCACATCGAGTAAAAAACCAAGATTCCACATTTTTCATAATATGTTTTAGTGTCTTAGGAATATTAAt                                                                                                                      >  2:244672/1‑141 (MQ=255)
                        ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                               >  1:194692/1‑141 (MQ=255)
                          agtagCCATTGGCATGGGGTTTGGCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                             <  2:252043/141‑1 (MQ=255)
                           gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                            <  1:656882/141‑1 (MQ=255)
                            aagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCATACAAAAAAGACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                           <  1:47773/140‑1 (MQ=255)
                             aggcATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATTAAAGTACAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                          <  2:370917/138‑1 (MQ=255)
                                    ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGGTTATCa                                                                                                   >  1:365685/1‑141 (MQ=255)
                                        tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAACAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                               <  1:317460/141‑1 (MQ=255)
                                                ttctcTTAGATAAAGCGTAAAAAAAATACTACAATAAAAGTACCAAATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                       <  2:319553/140‑1 (MQ=255)
                                                   tctcGGACAAAGCGTACAAAAAATCCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                    <  1:187783/141‑1 (MQ=255)
                                                   tctTCGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                    <  1:169966/141‑1 (MQ=255)
                                                   cctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                    <  1:65419/140‑1 (MQ=255)
                                                   cctTGGAAAAAGCGTACAAAAAATACTGCAATAAAAGTACGACATAGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                    <  2:486123/140‑1 (MQ=255)
                                                            aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                           >  1:62621/1‑141 (MQ=255)
                                                                gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATAATCACTTATCCTTGTATTTATAATTGAATTaa                                                                       >  1:586125/1‑141 (MQ=255)
                                                                        aaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACAAGCATCTATATCCCGGGGAATATGGTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatat                                                               >  1:164165/1‑141 (MQ=255)
                                                                         aTACTTCAATTAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                                              <  2:373659/141‑1 (MQ=255)
                                                                         aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                                              <  2:308635/141‑1 (MQ=255)
                                                                                        tACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTg                                               >  1:606946/1‑141 (MQ=255)
                                                                                         aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                              >  1:173472/1‑141 (MQ=255)
                                                                                           cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                            <  2:138698/141‑1 (MQ=255)
                                                                                             caTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGTTCGTCGTGCTaaa                                          >  1:579893/1‑141 (MQ=255)
                                                                                                    tAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                                   >  2:659121/1‑141 (MQ=255)
                                                                                                         aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTTAAGATCGTCGTGCTCAACAATAATGCACt                              <  1:371932/141‑1 (MQ=255)
                                                                                                             cagcagCTGTATCACTCTTAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                          <  2:354322/141‑1 (MQ=255)
                                                                                                             cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                          <  2:448711/141‑1 (MQ=255)
                                                                                                               gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAACGt                        >  2:168639/1‑141 (MQ=255)
                                                                                                               gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                        >  2:52295/1‑141 (MQ=255)
                                                                                                               gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                        >  2:661220/1‑141 (MQ=255)
                                                                                                               gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTGATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                        >  2:498274/1‑141 (MQ=255)
                                                                                                                          aCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACATTAATGCACTTAAAGTTTTGAACTGAc             <  2:433198/141‑1 (MQ=255)
                                                                                                                                 atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt      <  1:659121/141‑1 (MQ=255)
                                                                                                                                  tatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAGGAAATTTa     >  2:316753/1‑141 (MQ=255)
                                                                                                                                  tatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTa     >  2:539898/1‑141 (MQ=255)
                                                                                                                                   atGTTTTCTTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc    <  2:476431/141‑1 (MQ=255)
                                                                                                                                     gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACaa  >  2:670047/1‑141 (MQ=255)
                                                                                                                                     gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACaa  >  2:670145/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                        
AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513793‑1514066

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑