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% 57.3 / NA 19L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (12/7);  total (12/7)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTG  >  USA300TCH1516_ALE/1513793‑1514053
                                                                                                                                         |                                                                                                                            
aaTTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGAGAAAAAAAAATACGTCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTGTTAtt                                                                                                                           >  2:249883/1‑141 (MQ=255)
       ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                    >  1:254191/1‑141 (MQ=255)
                           gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                >  2:210288/1‑141 (MQ=255)
                            tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                               <  2:120009/141‑1 (MQ=255)
                             agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                              >  2:161560/1‑141 (MQ=255)
                                  ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                         <  1:396268/141‑1 (MQ=255)
                                    ggaaTGGGGTTTGTCGGCTGGATAAAGGGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                       <  2:60140/138‑1 (MQ=255)
                                    ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                       >  1:174746/1‑141 (MQ=255)
                                        tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                   >  2:392359/1‑141 (MQ=255)
                                                            aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACGAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTGTCACTTATCCTTG‑TATTTATCTTTGaa                                                              >  2:260640/1‑141 (MQ=255)
                                                                     aaaaaTACTGAAATAAAATTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAAtatta                                                     >  2:51858/1‑141 (MQ=255)
                                                                                 aTAAAAGTATCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGAt                                         <  2:10943/141‑1 (MQ=255)
                                                                                        tACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTg                                  >  1:401477/1‑141 (MQ=255)
                                                                                          ccACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                >  1:266594/1‑141 (MQ=255)
                                                                                              aTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAGTACCAATAATTGGA‑TAGCGGTTATTTTTGTTATTTATAATTGAATTAATATTATATATTAAAGATTGTCGTTCTaaat                            >  2:293314/1‑140 (MQ=255)
                                                                                                         aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                 <  1:11916/141‑1 (MQ=255)
                                                                                                            ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa              <  2:174746/141‑1 (MQ=255)
                                                                                                                  tCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtttt        >  1:166130/1‑141 (MQ=255)
                                                                                                                        tCACTCATAATATGTTTTATTGTATTAAGATTATTAATGCCATTATTTGGCTTTTACGCTGGCCGGG‑AATTTGTGATGGAAGTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTg  <  2:186981/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                            
AATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTG‑TATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTG  >  USA300TCH1516_ALE/1513793‑1514053

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: ‑