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% 138.5 / ‑6.5 47L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (24/22);  total (24/23)
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.

ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513794‑1514062
                                                                                                                                        |                                                                                                                                    
atttaattGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGATTTTCACTTGGATAAAGCGCACAAAAAATACTGTAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACACATAATATGTTGTATTg                                                                                                                                  >  2:56826/1‑141 (MQ=255)
   tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                               <  1:235971/141‑1 (MQ=255)
          atgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTAAAAAAACAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                        <  2:653570/141‑1 (MQ=255)
             tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                     <  1:491633/141‑1 (MQ=255)
             tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCATACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                     >  1:456748/1‑141 (MQ=255)
              atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAGTAGGAttatta                                                                                                                    >  1:690949/1‑141 (MQ=255)
                     tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTCTATCACTCATAATCTGTTTTATTGTATTAGTATTATTAATACCat                                                                                                             >  1:211751/1‑141 (MQ=255)
                       ttaGTAGCCATTGGCATTGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                           <  2:725390/141‑1 (MQ=255)
                         agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                         >  2:201474/1‑141 (MQ=255)
                         agtacCCATTGGCATGGGGTTTGTCTCTTGCATAAAGCGTACAAAAAATACTGCCATAAAAGTACCACATCCCGTAAAAAAACCAGCATCTATATCACTCATAATATGTGTTATTGTATTAGGATTATTAATGCCataatg                                                                                                         >  2:480456/1‑140 (MQ=255)
                           tgaccATTGGCATTGGGTTTGTCCTTTCGAGACATAGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTACGATTACTAATGCCATTATTTg                                                                                                       <  2:357199/138‑1 (MQ=255)
                            agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                      >  2:191825/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                 >  2:498817/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAGATCGCGTAAAAAAACCAGCATCTATATAACTCATAATATGTTTTATTCTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                 >  2:440981/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTAACAGATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTATATTAGGATTATTAATGCCATTATTTggtatat                                                                                                 >  2:440937/1‑136 (MQ=255)
                                 ttGGCATGGGGCTTGTCTCTTGGATAAAGCGTACAAAAAANACTGCAATACAAGTACCACATCGCGTAAAAAAACCCGCATCTCTATCACACATAATATGTTTNCTGGTATCAGGATTATTAATGCCATTATTTGGTTTAt                                                                                                 >  2:571856/1‑141 (MQ=255)
                                      aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                            >  2:513458/1‑141 (MQ=255)
                                               gTCTCTTGGATATAGCGTACAAAAAATACTGCACTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATACTATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGTATTATCACTTATCCTTGTa                                                                                   <  2:441572/141‑1 (MQ=255)
                                                 ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCAATCATAATATGTTGTATTGTATTAGGATTATTAATGCCATTATTTGGATGATCACTTATCCTTGtttt                                                                                 >  1:46404/1‑141 (MQ=255)
                                                    ttGGATAAAGCGTATAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                                              >  1:435420/1‑141 (MQ=255)
                                                      ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                            <  1:358726/141‑1 (MQ=255)
                                                      ggATAAAGCCGACAACAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGCATTATTTATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                            <  2:511776/141‑1 (MQ=255)
                                                       gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                           <  1:630490/141‑1 (MQ=255)
                                                       gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                           <  1:346573/141‑1 (MQ=255)
                                                           aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGat                                                                       >  2:250209/1‑140 (MQ=255)
                                                           aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATAACTTATCCTTGTATTTATAATTGaa                                                                       >  2:616480/1‑141 (MQ=255)
                                                               gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTaa                                                                   <  1:772738/141‑1 (MQ=255)
                                                                     aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTTTAATTGAATTAAtattat                                                             >  1:501637/1‑141 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                                          <  1:191825/141‑1 (MQ=255)
                                                                         tACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTatatat                                                         >  2:369218/1‑141 (MQ=255)
                                                                              cAATAAAAGTACCACATCTCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAg                                                    <  2:471118/141‑1 (MQ=255)
                                                                               aaTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                                   <  1:108496/141‑1 (MQ=255)
                                                                                aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAt                                                  <  1:530631/141‑1 (MQ=255)
                                                                                    aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtc                                              <  1:101308/141‑1 (MQ=255)
                                                                                           acaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                       <  1:524663/141‑1 (MQ=255)
                                                                                            caTCGCGTAAAAAAACAAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCAATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaaa                                      >  2:242646/1‑141 (MQ=255)
                                                                                                  gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAATATCGTCGTTCTAAACaataa                                <  1:352385/141‑1 (MQ=255)
                                                                                                   tAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                               >  2:479375/1‑141 (MQ=255)
                                                                                                        aaaCCAGCATCTATATCACACATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                          <  1:129744/141‑1 (MQ=255)
                                                                                                         aaCCAGCCTCTATATCACTCATAATATGTTTAAATGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGACTTAATATTATATATTAAAGATCGTCGTGCTAAACAAGAATGCACtt                         <  1:523146/141‑1 (MQ=255)
                                                                                                         aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTGAACAATAATGCACtt                         >  2:320162/1‑141 (MQ=255)
                                                                                                          aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                        >  1:681638/1‑141 (MQ=255)
                                                                                                                    atatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGaa              <  1:196922/141‑1 (MQ=255)
                                                                                                                          cTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACg        <  1:679664/141‑1 (MQ=255)
                                                                                                                            cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaa      >  2:759201/1‑141 (MQ=255)
                                                                                                                            cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaa      >  1:786861/1‑141 (MQ=255)
                                                                                                                             ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa     <  1:16978/141‑1 (MQ=255)
                                                                                                                                atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCATTGTATTTTTAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGGCGAAAttt  >  2:301597/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                    
ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513794‑1514062

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: ‑