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% 149.7 / NA 48L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (20/28);  total (20/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGA  >  USA300TCH1516_ALE/1513811‑1514054
                                                                                                                       |                                                                                                                            
gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                <  1:526651/134‑1 (MQ=255)
   gtattaGTAGCCATTGGCATGGGGTTTGTCTCGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACAGCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                             <  1:418208/133‑1 (MQ=255)
       tagtagGCAGAGGCACGGGGGTAGACGCGTCGAGAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAAACGAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                         <  1:331068/134‑1 (MQ=255)
       gagtagCCAGTGGAATGGGGTTTGTCTCTGGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                         <  1:493774/133‑1 (MQ=255)
        agtagCCATTGGCATGTGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGc                                                                                                        <  1:271761/134‑1 (MQ=255)
         gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTATTGcc                                                                                                       >  1:432407/1‑134 (MQ=255)
             ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                   <  2:89752/134‑1 (MQ=255)
                tttgCATTGAGTTTTTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                <  1:107822/131‑1 (MQ=255)
                        gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                        >  2:54684/1‑134 (MQ=255)
                          gTTTGTCTCTTGTATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                      <  1:161627/134‑1 (MQ=255)
                          gTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                      <  2:153316/134‑1 (MQ=255)
                            ttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAATAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                    <  1:52835/134‑1 (MQ=255)
                             tGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                   >  2:163982/1‑134 (MQ=255)
                             tGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAATTGGATTATCACTTa                                                                                   >  2:133592/1‑134 (MQ=255)
                              gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCCCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGCATTTTcctctat                                                                                  >  2:185485/1‑128 (MQ=255)
                                ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATTTCACTCATAATATGTTTTATTTTATTAGGATTATTAATGACATTATTTGTATTATTATTTATcc                                                                                >  1:18148/1‑134 (MQ=255)
                                 tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                               <  1:430282/134‑1 (MQ=255)
                                       aTAAAGCGTACAAAAAATACTGAAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                         <  2:297049/134‑1 (MQ=255)
                                        tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                        <  1:594256/134‑1 (MQ=255)
                                        tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGGTTTATTGTATCAGGATTATTAATGCCATTATTTGTATTATCACTTATCCTTGTAttt                                                                        <  1:594237/134‑1 (MQ=255)
                                            gagTACAAAAAATACTACAATAAAAGTACCACATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                    <  2:601244/132‑1 (MQ=255)
                                            gCGGACAAAAAATACTGCAATAAAAGTACCACATCGGGTAAAAATACTGGCTTCTATATGAGTCTTATTATGTTTTATTGTATTAGGATTAGGAGTTGCATTTTTTGGATTATGACTTATCCTTGTATTTATaa                                                                    <  2:103371/134‑1 (MQ=255)
                                                aCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGTATAACACAAATCCTTGTATTTATAATTGa                                                                >  1:162838/1‑134 (MQ=255)
                                                   aaagaTACTGCAATAAAAGGACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                             <  1:534855/134‑1 (MQ=255)
                                                   aaaaaTACTTCAATAAAAGTACCACATAGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                             <  2:7323/134‑1 (MQ=255)
                                                   aaaaaTACTGCAATAAAAGTACCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                             <  2:561416/134‑1 (MQ=255)
                                                   aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTCGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                             >  1:566112/1‑134 (MQ=255)
                                                   aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACGCAAAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                             <  1:125428/134‑1 (MQ=255)
                                                    aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTTTCACTTATCCTTGTATTTATTATTGAATTa                                                            >  1:161853/1‑134 (MQ=255)
                                                     aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATTACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTaa                                                           <  2:524347/134‑1 (MQ=255)
                                                     aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTaa                                                           >  2:375918/1‑134 (MQ=255)
                                                         aCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatt                                                       <  1:111900/134‑1 (MQ=255)
                                                          cTGGAATAAAATTACCACATCGCGTAAAATAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                      <  2:566112/134‑1 (MQ=255)
                                                                tAAAAGTACCACATCGCGTAATAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                <  1:266504/134‑1 (MQ=255)
                                                                    aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTCGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaaa                                            >  1:168370/1‑133 (MQ=255)
                                                                      tACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAt                                          >  2:520684/1‑134 (MQ=255)
                                                                         cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                       >  1:128370/1‑134 (MQ=255)
                                                                                        aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                        >  1:351326/1‑134 (MQ=255)
                                                                                             gCATCTTTAGCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAc                   <  1:503735/134‑1 (MQ=255)
                                                                                             gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTTTATATTTCAGATCGTCGTACTAAACAATAATGCAc                   >  2:124958/1‑134 (MQ=255)
                                                                                             gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTTCTAAACAATAATGCAc                   >  2:385670/1‑134 (MQ=255)
                                                                                             gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAc                   <  2:409686/134‑1 (MQ=255)
                                                                                               aTCTATTTCACTCATCTTATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                 <  1:17173/134‑1 (MQ=255)
                                                                                                    tatCACCCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTACATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt            >  2:511232/1‑134 (MQ=255)
                                                                                                        aCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGATTTAATATTATATATTACATCTCTTCTTTCTGAACTATAATGTCATTAAACTTTTg        >  2:608154/1‑134 (MQ=255)
                                                                                                          tCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGaa      <  2:432407/134‑1 (MQ=255)
                                                                                                             taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATAGTCGTGCTAAACAATAATACACTTAAAGTTTTGAACTg   >  1:555920/1‑134 (MQ=255)
                                                                                                              aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGa  >  2:62770/1‑134 (MQ=255)
                                                                                                                       |                                                                                                                            
GCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGA  >  USA300TCH1516_ALE/1513811‑1514054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑