Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,909,486:1 +T 100% coding (293/303 nt) USA300HOU_RS09460 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,909,4861.T100.0% 97.1 / NA 30G98V (GGT→GTT) USA300HOU_RS09460hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (12/18);  total (12/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGC  >  USA300TCH1516_ALE/1909347‑1909621
                                                                                                                                            |                                                                                                                                       
ttGTCTATAATTTTTGCAGATCGTTCAATGAAATCACGAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑t                                                                                                                                        <  1:114589/141‑1 (MQ=255)
       taATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑tttttatt                                                                                                                                 >  1:5859/1‑137 (MQ=255)
         aTTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTtttattta                                                                                                                                >  1:144459/1‑141 (MQ=255)
                         cAAGTAAATCACTAAAGCCTGATGCAGATTTGACTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTCTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTc                                                                                                                <  1:411422/141‑1 (MQ=255)
                           aTTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAATAAAGTTAATATGTCAt                                                                                                              >  1:369774/1‑141 (MQ=255)
                                   aCTAAAGCCCGATGCAGATTGGATTAGAATTGAGCTTGCTTTGGTTCTTTGGCTTGATCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGcat                                                                                                      >  1:638026/1‑139 (MQ=255)
                                         gcatGATGCAGATTGGATTAGGATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATAc                                                                                                <  1:408109/138‑1 (MQ=255)
                                                gCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaa                                                                                         <  1:94030/141‑1 (MQ=255)
                                                     ttGGATTAGAATTGCGTGTAAAAGTTTGACTTGGATTATTCTAAAACTTGATAAATAACATAGCTTTCCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaatacaa                                                                                    <  1:377203/141‑1 (MQ=255)
                                                     ttGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaatacaa                                                                                    <  1:656724/141‑1 (MQ=255)
                                                       ggATGAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATg                                                                                  <  1:78923/141‑1 (MQ=255)
                                                                  gCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCCTGCtat                                                                       >  1:358828/1‑141 (MQ=255)
                                                                       tAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGa                                                                  <  1:13416/141‑1 (MQ=255)
                                                                       tAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGa                                                                  <  1:13196/141‑1 (MQ=255)
                                                                         aaaGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGt                                                                <  1:144112/141‑1 (MQ=255)
                                                                          aaGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTa                                                               <  1:322474/141‑1 (MQ=255)
                                                                                  cTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAAtt                                                       <  1:223658/141‑1 (MQ=255)
                                                                                        ttattCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATaa                                                 <  1:84111/141‑1 (MQ=255)
                                                                                        ttattCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGGAAAACAATTTGCTaa                                                 >  1:793163/1‑141 (MQ=255)
                                                                                                    ttATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGta                                     >  1:871196/1‑141 (MQ=255)
                                                                                                       ttttAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATaa                                  >  1:480383/1‑141 (MQ=255)
                                                                                                         ttAGTACATATCTTTTAAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATaaaa                                <  1:21700/141‑1 (MQ=255)
                                                                                                            gTACATATCTTTTCTATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAat                             >  1:569103/1‑141 (MQ=255)
                                                                                                              gcacatCTTTCGAAGTGGTCGGACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAatat                           <  1:825443/137‑1 (MQ=255)
                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   <  1:730442/141‑1 (MQ=255)
                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   <  1:870050/141‑1 (MQ=255)
                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   >  1:272082/1‑141 (MQ=255)
                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             >  1:659214/1‑141 (MQ=255)
                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             <  1:295878/141‑1 (MQ=255)
                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             >  1:286966/1‑141 (MQ=255)
                                                                                                                              gTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGGTAACGTTGTTGCGTATAAAAAATATTCGATTTTCGCAAGCa           >  1:108347/1‑141 (MQ=255)
                                                                                                                                       ttCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGc  <  1:244845/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                       
TTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGC  >  USA300TCH1516_ALE/1909347‑1909621

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑