Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,513,930 A→T 100% L413F (TTA→TTT)  USA300HOU_1379 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,513,9300AT100.0% 136.0 / ‑6.5 42L413F (TTA→TTT) USA300HOU_1379hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (16/25);  total (17/25)
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.

ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513798‑1514064
                                                                                                                                     |                                                                                                                                      
atttTTATGGATCGCTGTAGTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                <  2:518192/141‑1 (MQ=255)
   tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGAAAAAGCAAACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                             <  2:381032/141‑1 (MQ=255)
   tgtatgtaTCACTTTATTAGTAGCCATTGGCATGGGGTTTGCCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACAAAAAAACAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                             <  2:528432/141‑1 (MQ=255)
               tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGAAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATCAGGATTATTAATGcc                                                                                                                 <  1:335773/141‑1 (MQ=255)
                 taatacaaacaaTTAGCATGGGGCTTTACTCTTGGAAAAAAAAAAAAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                               <  2:398643/130‑1 (MQ=255)
                     acgagCCATCGGCATGGGGTTTGTCTCTTGAATAAAGCGTACAAAAAATACCTCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                           <  2:346880/138‑1 (MQ=255)
                       tagCCATTGGCATGGGGTTTGTCTCTTGGAGAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                         <  2:145630/141‑1 (MQ=255)
                        agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACCCATAATATGTTTTATTGTATTCGGATTATTAATGCCATTATTTgg                                                                                                        >  1:4053/1‑141 (MQ=255)
                         gCCATTGGCATGGAGTTTGTCTCTTGGACACAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                       <  2:430267/141‑1 (MQ=255)
                             ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAACTACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTAGATCGCTCGGAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                   <  2:435694/141‑1 (MQ=255)
                               tgCATGGCGTTTGTCTCCTGGATAAAGAGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCTTAAAAAAATCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 <  2:431652/140‑1 (MQ=255)
                               ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 >  1:398411/1‑141 (MQ=255)
                               ggCATGGGGTTTGTCTCATGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCATAAAAAAACCAGCATCTATCTCACTCATAATATGTTTTATTGTATAAGGATTATTAATGCCATTATTTGGATGATCa                                                                                                 >  2:542614/1‑141 (MQ=255)
                                gCATGGGGTTTGTTTGTTGTATAAAGCGTACAAAAAATACTGCAAAAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                <  2:475740/141‑1 (MQ=255)
                                  aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                              >  1:77026/1‑141 (MQ=255)
                                    ggggTTTGTCTCTTGGATAAATCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                            <  1:613093/141‑1 (MQ=255)
                                        tttGTCTCTTGGATAAAGCGTACAAAAAATACGGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATGAGGATTATTAATGCCATTATTTGGAGTTTCACTTATCCtt                                                                                        >  2:5696/1‑141 (MQ=255)
                                            tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  1:517356/141‑1 (MQ=255)
                                              tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                  <  1:390576/141‑1 (MQ=255)
                                                     tAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                           <  1:229189/141‑1 (MQ=255)
                                                     tAAAGCGAACAAAAAATACTGCAAAAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                           <  2:261863/141‑1 (MQ=255)
                                                      aaaGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                          >  2:587963/1‑141 (MQ=255)
                                                        aGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        >  2:465335/1‑141 (MQ=255)
                                                           gaaCAAAAAATACTGCAATAAAAGCTACAAC‑TCGAGTAAAAAAACCAGCATTTATAGCACTCATATTATTTTTTATGTTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATGGAATTaa                                                                     <  2:294363/139‑1 (MQ=255)
                                                                aaaaaTACTGCAATAAAAG‑GACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                <  2:160649/141‑1 (MQ=255)
                                                                         gCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTCCCCTTGTGTTTATAATTGAATTAATATTATATATTaaa                                                       <  1:95249/141‑1 (MQ=255)
                                                                         gCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                       <  1:371533/141‑1 (MQ=255)
                                                                           aaTAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTGATCCTTGTATTTATAATTGAATTAATATTATATATTCAAGa                                                     <  1:456510/141‑1 (MQ=255)
                                                                                 aG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg                                               >  2:22433/1‑141 (MQ=255)
                                                                                 aG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg                                               >  1:270530/1‑141 (MQ=255)
                                                                                  g‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATcgccgt                                              >  1:95566/1‑141 (MQ=255)
                                                                                      ccACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                           <  2:618112/141‑1 (MQ=255)
                                                                                                tAAAAAAACCAGCATCTATATCACTAATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                                 <  2:83576/141‑1 (MQ=255)
                                                                                                  aaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGc                               >  2:583618/1‑141 (MQ=255)
                                                                                                    aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAACCAATAATGCAc                             >  1:39767/1‑141 (MQ=255)
                                                                                                    aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAc                             <  2:379811/141‑1 (MQ=255)
                                                                                                                     cACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGa            <  1:15168/141‑1 (MQ=255)
                                                                                                                            aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt     >  2:335752/1‑141 (MQ=255)
                                                                                                                             atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt    >  2:390744/1‑141 (MQ=255)
                                                                                                                             atatGTTTAATTGTATTAGGAAGATTAATGCCATTATTTGGATTATCACTGAGCCTAGTATTTATAATTGAATTAATATTAAATATTAAATATCGTCGTGCTTGAAAATAATGAACTTAAAGTTTTGAACTAACGAAAatt    >  2:227697/1‑141 (MQ=255)
                                                                                                                               atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAGTTTAc  >  1:221236/1‑141 (MQ=255)
                                                                                                                               atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  >  1:551667/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                      
ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAG‑TACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513798‑1514064

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: ‑