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_ALE1,513,9300AT96.0% 77.0 / ‑3.6 25L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (12/12);  minor base C (0/1);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTA  >  USA300TCH1516_ALE/1513795‑1514063
                                                                                                                                       |                                                                                                                                     
tttatttGTATGTATCGCGTCATTAGGAGCCATTGGTATGGGGTTTGTCTCTTGGATAAAGCTTATAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTg                                                                                                                                   <  1:158910/140‑1 (MQ=255)
                gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                   <  1:207156/140‑1 (MQ=255)
                     attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                              >  2:146707/1‑140 (MQ=255)
                      ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatt                                                                                                             >  2:151618/1‑140 (MQ=255)
                      ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatt                                                                                                             >  2:107690/1‑140 (MQ=255)
                              cATTGGCATGGGGTTTGTCTCTTGGATAAAACATAAAAAAAATACTGAAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAt                                                                                                     <  2:39818/140‑1 (MQ=255)
                                    cATTGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTAACACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTCATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                               <  2:358212/140‑1 (MQ=255)
                                    cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                               >  1:74914/1‑140 (MQ=255)
                                         ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                          >  1:412212/1‑140 (MQ=255)
                                                 tctTTGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                  <  1:366916/140‑1 (MQ=255)
                                                 tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                  <  1:194856/140‑1 (MQ=255)
                                                   ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAATAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                <  1:33775/140‑1 (MQ=255)
                                                   ttGAATAAAGCGTACAAAAAATACTGAAATAACAGTCCCATATCGCGTAAAAATACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCTCTTATCCTTGTATTta                                                                                <  2:343902/140‑1 (MQ=255)
                                                            gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTTATATAACCGGTATCTAGATCACTCATGGTATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                       <  1:345341/140‑1 (MQ=255)
                                                                     aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                              <  2:317268/140‑1 (MQ=255)
                                                                            gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTac                                                       >  2:158534/1‑139 (MQ=255)
                                                                                   aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                <  2:109896/140‑1 (MQ=255)
                                                                                   aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTACTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                <  1:284464/140‑1 (MQ=255)
                                                                                       aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTAAATATTAAAGATCGTCGTg                                            >  1:229670/1‑140 (MQ=255)
                                                                                                             gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg                      >  2:506991/1‑140 (MQ=255)
                                                                                                                 cTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTTTTTGGTTTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtttt                  >  1:456790/1‑140 (MQ=255)
                                                                                                                 cTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtttt                  >  1:69179/1‑140 (MQ=255)
                                                                                                                              aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt     <  1:180584/140‑1 (MQ=255)
                                                                                                                              aataTGTTTTATTGTATTAGGATTATTAATACCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACAGACGAAAt     >  2:446108/1‑140 (MQ=255)
                                                                                                                                 atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATTATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGCAGAAATTTa  >  1:354936/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                     
TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTA  >  USA300TCH1516_ALE/1513795‑1514063

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: ‑