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% 82.8 / NA 29L413F (TTA→TTT) USA300HOU_1379hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (20/9);  total (20/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  CP000730/1513798‑1514064
                                                                                                                                    |                                                                                                                                      
atgtggatgtatCGCTTTATGAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACACATAATATGTTTTATTGTAtt                                                                                                                                >  2:379462/7‑141 (MQ=255)
          atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGAttatta                                                                                                                      <  2:48710/141‑1 (MQ=255)
            cgatttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAACTACTGCAATAAAAGTACCACATTGCGTAAAAAAACCAGCCTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                    >  2:196658/4‑141 (MQ=255)
                 tatgggtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                               <  1:301025/136‑1 (MQ=255)
                        tgCCAGTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                        <  2:362827/140‑1 (MQ=255)
                                   tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                             >  2:233683/1‑141 (MQ=255)
                                        tttGTCTCTTGGATAAAGCGTACAAAAAATACTGCATGAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATtatcctttatcctt                                                                                        >  2:191334/1‑141 (MQ=255)
                                            tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAATTACCACATCGCGTAAAAAGACCAGGATCTATATCACTCATAATATGTTTTATTGTATTAGGTTTATTAATGCCATTATTTGGATTATCACTTATCCTTGTag                                                                                    <  2:5430/141‑2 (MQ=255)
                                              tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                  <  2:342428/141‑1 (MQ=255)
                                                  ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCCGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAATATCACTTATCCTGGTATTTATaa                                                                              >  1:90757/1‑141 (MQ=255)
                                                  ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTCTTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                              >  1:229381/1‑141 (MQ=255)
                                                       aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                         >  1:177896/1‑141 (MQ=255)
                                                             aCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAatt                                                                   >  1:67767/1‑140 (MQ=255)
                                                             aCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAatt                                                                   >  1:8351/1‑140 (MQ=255)
                                                             aCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                   >  2:9770/1‑141 (MQ=255)
                                                                aaacaTACTGCAATTAAAGTACCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                <  1:243925/141‑1 (MQ=255)
                                                                      aCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                          >  1:303382/1‑141 (MQ=255)
                                                                      aCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTCATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                          >  1:211770/1‑141 (MQ=255)
                                                                       cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                         >  1:286000/1‑141 (MQ=255)
                                                                        tGCAATAAAAGTACCACATCGCGTAAAAAACACAGCATCTCTATTAATCTTGTCATTTTATATTATATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTCTTTATAATTGAATTAATATTATATATTaa                                                        >  2:269955/1‑141 (MQ=255)
                                                                        tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCATTGAATTAATATTATATATTaa                                                        >  2:362065/1‑141 (MQ=255)
                                                                                     ccACATCGCGTAAAAAAACAAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTTGTGCt                                           >  1:282057/1‑141 (MQ=255)
                                                                                        caTCGCGTAAAAAAACCAGCAGCTACATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTCGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATGAAAGATCGTCGTGCTaaa                                        <  2:6674/141‑1 (MQ=255)
                                                                                                      aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAACGGTAGTTGAGCTAAACAATAATGCAATTa                          >  2:364520/1‑141 (MQ=255)
                                                                                                            aTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGttt                    <  1:218171/141‑1 (MQ=255)
                                                                                                                     aCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc           >  2:77102/1‑141 (MQ=255)
                                                                                                                        cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAGATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaa        <  2:118646/141‑1 (MQ=255)
                                                                                                                            atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt    >  2:59567/1‑141 (MQ=255)
                                                                                                                              atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  >  2:151775/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                      
ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  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: ‑