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
*CP0007301,513,9300AT97.9% 159.3 / ‑5.9 51L413F (TTA→TTT) USA300HOU_1379hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (23/26);  minor base C (2/0);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 2.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
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.

TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  CP000730/1513795‑1514065
                                                                                                                                       |                                                                                                                                       
tttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGt                                                                                                                                    <  1:345410/141‑1 (MQ=255)
tttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGt                                                                                                                                    <  1:165150/141‑1 (MQ=255)
  tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                  >  1:249110/1‑141 (MQ=255)
  tatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGCGTTTGTCTCGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                  <  1:646228/141‑1 (MQ=255)
                  tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                  >  2:423169/1‑141 (MQ=255)
                   ttattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTTCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                                 <  1:157624/141‑1 (MQ=255)
                   ttattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                                 <  1:104183/141‑1 (MQ=255)
                   ttactaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                                 <  1:835289/141‑1 (MQ=255)
                               aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTCGGATTATTAATGCCATTGTTTGGAtga                                                                                                     >  1:239327/1‑139 (MQ=255)
                                 tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAtt                                                                                                   >  2:772517/1‑140 (MQ=255)
                                 tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                   >  1:361447/1‑141 (MQ=255)
                                  ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTTTTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                  >  1:20445/1‑141 (MQ=255)
                                  ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                  >  2:452799/1‑141 (MQ=255)
                                  ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                  >  2:515240/1‑141 (MQ=255)
                                  ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                  >  2:515156/1‑141 (MQ=255)
                                   gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCCTAATATATTTTATTGTATTAGTATTATTAATTCCATTATTTAGATTATCat                                                                                                 >  1:697118/1‑140 (MQ=255)
                                   gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                 <  2:425529/141‑1 (MQ=255)
                                     aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                               >  1:537858/1‑141 (MQ=255)
                                           tttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTCATTGTATTCGGATTATTAATGCCATTAGTTGGATTATCACTTCTCCtt                                                                                         >  2:162644/1‑141 (MQ=255)
                                              ttctcGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCAGAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                      <  1:472371/140‑1 (MQ=255)
                                                 tctTGGATAAAGCCTACAAAAAATTCTTCAAGAAAATTACCACATCGCGTAAAAAAACCAGCATCTATATCACCCATAATATGTTTTATTGTATTAGGATTAATAATTCCACTATATGGATTATTAATTATTCTTGTAtct                                                                                   >  2:465312/1‑139 (MQ=255)
                                                     ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                               <  1:400148/141‑1 (MQ=255)
                                                      gaaaaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAACCCAGCATCTATATCACTCATATTATGTTTTATTGTATTAGGATTATTAATGCCAGTATTTGGATTATCACTTATCCTTGTATTTATaac                                                                              <  1:100752/138‑2 (MQ=255)
                                                          aggCGTACAAAAAATACTGCGATAAGAGCACCAAATGCCGTAAAAAAATCAGCGTCTATATCACTCATAATATGTTTTCTTGTATTAGGATTATTAATGCCATTATTTGGTTTATCACTTATCCTTGTATTTATAATTGaa                                                                          <  2:338748/139‑1 (MQ=255)
                                                          aagctcaCAAAAAATACTGCAATAAAAGGACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                          <  1:59642/135‑1 (MQ=255)
                                                           aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                         >  1:251675/1‑141 (MQ=255)
                                                            gCGTACAAAAAATACTGCAATAAAAGTACCACATCGGGCAAAAAAAACAGCATCTATTTCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                        >  1:402251/1‑141 (MQ=255)
                                                            gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                        <  2:249110/141‑1 (MQ=255)
                                                                           ttgcataataGTACCACATCGCGTAAAAAATCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAGATTATATATTaa                                                         <  2:571896/137‑1 (MQ=255)
                                                                             cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAg                                                       >  2:787369/1‑141 (MQ=255)
                                                                              aaTAAAAGTACCACATCGCGTAAAAACACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGAGTATTAATGCAATTATTTTGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                                      <  1:158869/141‑1 (MQ=255)
                                                                                   aaGTACCACATCGCGTAAAAAAACCAGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtc                                                 <  2:674520/141‑1 (MQ=255)
                                                                                       aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                             <  1:723175/141‑1 (MQ=255)
                                                                                             tCGCGTAAAAAAACCAGCCTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                       <  2:68063/141‑1 (MQ=255)
                                                                                                    aaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGTTCGTCGTGCTAAACAATATTGc                                >  1:62197/1‑141 (MQ=255)
                                                                                                     aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATCTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                               <  1:565522/141‑1 (MQ=255)
                                                                                                      aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAc                              <  2:820645/141‑1 (MQ=255)
                                                                                                       aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTTAATTAATCTTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                             <  2:524084/141‑1 (MQ=255)
                                                                                                        agccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTCTACTTGATTGTGGATTATAGACTAAAGATCGTCGTGCTAAACAATAATGCACtt                            <  1:493527/139‑1 (MQ=255)
                                                                                                        aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTGTTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                            >  2:534936/1‑141 (MQ=255)
                                                                                                        aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                            <  1:277853/141‑1 (MQ=255)
                                                                                                        aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                            <  1:277857/141‑1 (MQ=255)
                                                                                                           cAGCATCTATATCACTCATAATATGTAGCAATGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                         >  1:615862/1‑141 (MQ=255)
                                                                                                             gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGt                       >  2:650250/1‑141 (MQ=255)
                                                                                                              cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                      >  2:321397/1‑141 (MQ=255)
                                                                                                              cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                      >  2:740656/1‑141 (MQ=255)
                                                                                                              cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                      <  2:772917/141‑1 (MQ=255)
                                                                                                                tCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtttt                    >  2:195397/1‑141 (MQ=255)
                                                                                                                             taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATGTTAAAGATCGTCGTGTTAAACAATAATGCACTTAAAGTTTTATACTGACGAAAt       >  2:802495/1‑141 (MQ=255)
                                                                                                                                 atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc   >  2:446713/1‑141 (MQ=255)
                                                                                                                                  tGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACa  <  1:787369/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  CP000730/1513795‑1514065

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: ‑