Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_pgi 1,583,846 C→A 12.6% S38S (TCG→TCT)  safA ← two‑component system connector membrane protein, EvgSA to PhoQP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi1,583,8460CA12.6% 107.3 / 2.7 44S38S (TCG→TCT) safAtwo‑component system connector membrane protein, EvgSA to PhoQP
Reads supporting (aligned to +/- strand):  ref base C (25/13);  new base A (2/4);  total (27/17)
Fisher's exact test for biased strand distribution p-value = 1.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACAATAAAGTTTTTATCGATACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAGCGGATAACGTTAAAAA  >  NC_000913_3_pae_pgi/1583700‑1583994
                                                                                                                                                  |                                                                                                                                                    
aaaCAATAAAGTTTTTATCGATACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATATCTTGCAATGCGACCCATTTCTGAAATACTCAACTGATCAATTTCCGa                                                                                                                                                    >  2:770814/1‑149 (MQ=255)
      tAAAGTTTTTATCGATACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAAt                                                                                                                                              >  1:770024/1‑149 (MQ=255)
      tAAAGTTTTTATCGATACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAAt                                                                                                                                              >  1:623376/1‑149 (MQ=255)
            ttttATCTGTTCTTTTTTAACATTTCATATTTATAATTTGCTGCTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTAt                                                                                                                                        <  2:330456/149‑1 (MQ=255)
                aTCGATACTTTTGTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCCTGCAAACTATTAATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATAAATAGAAAAAAAAATGGCTATCAAc                                                                                                                                    <  2:814577/149‑1 (MQ=255)
                    aTACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTTATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGACATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTaa                                                                                                                                >  2:202550/1‑149 (MQ=255)
                          ttttAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCa                                                                                                                          <  1:387323/149‑1 (MQ=255)
                           tttAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAg                                                                                                                         <  1:494146/149‑1 (MQ=255)
                               aCATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGCACTGAGTAATATCGCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGtaat                                                                                                                     <  1:484793/149‑1 (MQ=255)
                               aCATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGtaat                                                                                                                     >  1:532463/1‑149 (MQ=255)
                                  tttCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCAGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAg                                                                                                                  >  2:984195/1‑149 (MQ=255)
                                         tttATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACca                                                                                                           >  1:394449/1‑149 (MQ=255)
                                             taATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAAt                                                                                                       >  2:1365/1‑149 (MQ=255)
                                                tttGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGc                                                                                                    >  1:58/1‑149 (MQ=255)
                                                   gctgctTGTTTTCAGCCCTGCAAACTATTGATAATTAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGGAAGTGTCAGTAATAAGACAACCACAATTGCAGa                                                                                                 <  2:79308/149‑1 (MQ=255)
                                                     tgtttgttTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACa                                                                                               >  1:951575/1‑149 (MQ=255)
                                                       tttgtttTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTTCCAAAAAAATGGCTATCAAAGTAAGTGTAATTAATAAGACAACCACAATTGCAGACATg                                                                                             >  1:367711/1‑149 (MQ=255)
                                                                aGCATTGCAAACGAGTAATAATGAAATGTGAAAGATATCTAGAAAAGAGAACCATTTCTGAGATACTCAGCTGAAAAAAAAAAAAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTta                                                                                    <  2:459023/149‑1 (MQ=255)
                                                                  ccgtGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTtata                                                                                  <  1:362195/146‑1 (MQ=255)
                                                                  ccTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTtata                                                                                  >  2:609634/1‑149 (MQ=255)
                                                                   ctggCAAACTATTGATAATGAAATGTATAAAATATTTTGGTATGCGATCTATTTCAGAAACAATACGCTGATACATGGCAATATAAATGCCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAg                                                                                 <  2:251719/146‑1 (MQ=255)
                                                                     tGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGtt                                                                               <  2:394449/149‑1 (MQ=255)
                                                                            tATTGATAATGAAATGTGCAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTTCAGACATGATTTCTTTATAGTTGTCTCtt                                                                        <  1:94406/149‑1 (MQ=255)
                                                                             aaagATAAAAAAATGGATAAAAACTCCTGCAATGGAATCCATTTATGAAATACTCAGCTGAAAAATAACAAAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCttt                                                                       <  2:542948/146‑1 (MQ=255)
                                                                                 aTAATGAAATGTGTAAGATCTGTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTta                                                                                    >  2:886442/1‑132 (MQ=255)
                                                                                 aTAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATACGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGt                                                                   <  1:884535/149‑1 (MQ=255)
                                                                                 aTAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTta                                                                                    <  1:886442/132‑1 (MQ=255)
                                                                                 aTAATGAAATGTGTAAGATCTATTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGt                                                                   >  2:884535/1‑149 (MQ=255)
                                                                                       aaaTGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACACTTGCAGACATGATTTCTTTATAGTTTTCTCTTTGCGTGAtttt                                                             >  1:145200/1‑149 (MQ=255)
                                                                                          tgtgTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGtt                                                          <  2:110570/149‑1 (MQ=255)
                                                                                            tgtAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCCCAATTGCAAACATGCTTTCTTTTTTGTTTTTCCTTTTCGTGATTTTGgttt                                                        >  2:226022/1‑149 (MQ=255)
                                                                                            tgtAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTTTCTCTTTTCTGGATTTTGtttt                                                        >  1:336396/1‑149 (MQ=255)
                                                                                              tAAGATCTCTTAAAATGCACATCATATGTGAAATACTCAGCTGATCAAACGCACCCAAAATAACTATTAGTTTTCATGTCAGTAATAAGACCACAACAATTACAGACATGATTTCTTTCTAGATACCCATTTGCGTGCTTTTGTTTGTc                                                      >  2:966375/1‑149 (MQ=255)
                                                                                                 gATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACt                                                   <  1:609634/149‑1 (MQ=255)
                                                                                                                gACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCAtt                                    >  1:843128/1‑149 (MQ=255)
                                                                                                                   ccATTTCTGAAATACTCAGCTGATAAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTTACTGTGGTCTCCTGCATTTCa                                 >  2:349352/1‑149 (MQ=255)
                                                                                                                        tgtGAAATACTTAACATATCAATTAACTAAAAAATGGTTATTAACGTAAGTGTTATTAATAAGACAAACACAGTTGAACACATGATTTCTTTATAATTGTCCCTTTGCGTGATTTTGTTTTTCTTTGTGGTCGCATGCATTTCACatat                            <  2:148966/147‑1 (MQ=255)
                                                                                                                           gAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTGGTCTCTTTGAGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTTAAATATGtt                         >  2:144213/1‑149 (MQ=255)
                                                                                                                                  tCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAg                  >  1:590804/1‑149 (MQ=255)
                                                                                                                                  tCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAg                  >  2:534300/1‑149 (MQ=255)
                                                                                                                                  tCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGGGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGAGTGATTTTGTTTTTCACTGTGGGCGCATGCATTTCAAATATGtttatttaa                  >  2:112095/1‑148 (MQ=255)
                                                                                                                                    aGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAGCg                >  2:729884/1‑149 (MQ=255)
                                                                                                                                         aTCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTATTTTTAACTATGGTCGCATGCATTTCAAATATGTTTATTTAACGGATaa           >  2:267829/1‑149 (MQ=255)
                                                                                                                                              ttGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAGCGGATAACGTTa      >  2:412049/1‑149 (MQ=255)
                                                                                                                                                  cGAAAAAATGGCTATCAACGTAAGTGTCAGTAATCAGACAACCACAATGGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCAATGTGGTCGCATGCATTTCAAATATGTTTATTTAACGGATAACATTaaaaa  >  1:290798/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                    
AAACAATAAAGTTTTTATCGATACTTTTTTAACATTTCATATTTATAATTTGCTGTTTGTTTTCAGCCTTGCAAACTATTGATAATGAAATGTGTAAGATCTCTTGCAATGCGACCCATTTCTGAAATACTCAGCTGATCAATTGCCGAAAAAATGGCTATCAACGTAAGTGTCAGTAATAAGACAACCACAATTGCAGACATGATTTCTTTATAGTTGTCTCTTTGCGTGATTTTGTTTTTCACTGTGGTCGCATGCATTTCAAATATGTTTATTTAGCGGATAACGTTAAAAA  >  NC_000913_3_pae_pgi/1583700‑1583994

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: ‑