Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000731 81 N→G 100% intergenic (–/‑151) – / → repA –/replication protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000731810NG100.0% 165.4 / ‑6.5 51intergenic (–/‑151)–/repA–/replication protein A
Reads supporting (aligned to +/- strand):  ref base N (0/0);  major base G (29/21);  minor base C (1/0);  total (30/21)
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.

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGA  >  CP000731/1‑216
                                                                                                                                           |                                                                                                                                        
gatatttatcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTaaa                                                                                                                                         >  2:414960‑M1/60‑141 (MQ=255)
 atatttatatagtgtttataaactcttgataaagctatattttcctttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGaa                                                                                                                                        >  2:3442‑M1/59‑141 (MQ=255)
     ttatcaagtgtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTg                                                                                                                                    >  2:101738‑M1/55‑141 (MQ=255)
      tatcaagggtttataatcccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGt                                                                                                                                   >  2:24764‑M1/54‑141 (MQ=255)
      tatcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGt                                                                                                                                   <  1:44732‑M1/88‑1 (MQ=255)
       atcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGtt                                                                                                                                  <  1:92289‑M1/89‑1 (MQ=255)
       atcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGATTTTGTAATAAAACGTTTAGAAACTGtt                                                                                                                                  <  2:195321‑M1/89‑1 (MQ=255)
                ttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTtatat                                                                                                                         <  2:121983‑M1/98‑1 (MQ=255)
                 tataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTtatata                                                                                                                        <  2:293642‑M1/99‑1 (MQ=255)
                 tataaacccttgataaagctatattttcacttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACATTTAGAAACTGTTTATTtatata                                                                                                                        <  1:119825‑M1/99‑1 (MQ=255)
                     aacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAAttt                                                                                                                    >  1:104284‑M1/39‑141 (MQ=255)
                           tgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATa                                                                                                             >  1:113764‑M1/33‑141 (MQ=255)
                            gataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATAc                                                                                                            >  1:347131‑M1/32‑141 (MQ=255)
                            aataaagctatattttcccttgtataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATAc                                                                                                            >  2:296390‑M1/32‑141 (MQ=255)
                               aaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTg                                                                                                         >  1:228606‑M1/29‑141 (MQ=255)
                                    tatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGtatta                                                                                                    >  2:402241‑M1/24‑141 (MQ=255)
                                       attttcagttttataagtttATTTAAAGGACTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATtatat                                                                                                 >  2:169055‑M1/21‑141 (MQ=255)
                                          ttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAAt                                                                                              <  2:117819‑M1/124‑1 (MQ=255)
                                           tcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATg                                                                                             >  1:367887‑M1/17‑141 (MQ=255)
                                            cccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGa                                                                                            <  1:138267‑M1/126‑1 (MQ=255)
                                              tttttagaagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCGAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGaat                                                                                          >  2:226805‑M1/14‑141 (MQ=255)
                                              cttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATTATTCTCG‑ATACTTGTATTATATAATGaat                                                                                          <  2:247669‑M1/128‑1 (MQ=255)
                                              cttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGaat                                                                                          >  2:356974‑M1/14‑141 (MQ=255)
                                               ttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGaata                                                                                         <  1:384425‑M1/129‑1 (MQ=255)
                                                  tataagtttATTTAAAGTGTTAGAATAAATTTAATATAACAAAAACCACATCTACTGGTAATAGTCGGGGTTTTGTAATAAATCGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAataata                                                                                      >  2:136664‑M1/10‑141 (MQ=255)
                                                             ttAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCaa                                                                           <  2:138267/141‑1 (MQ=255)
                                                                  gTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCAcc                                                                      <  2:365374/141‑1 (MQ=255)
                                                                   tGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATAGAATGAATAATATCTTAGTGCAAGCACCt                                                                     <  2:92289/141‑1 (MQ=255)
                                                                        taataaACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATc                                                                >  2:289409/1‑141 (MQ=255)
                                                                          ataaACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAt                                                              >  2:78025/1‑141 (MQ=255)
                                                                          ataaACTGAATAGAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTGCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAt                                                              <  2:45015/141‑1 (MQ=255)
                                                                              aCTTAATATAACAAAAACCCCAACTACTGGCAATAGTCGGGGTTTGGTAATAAAACGCTTACAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCCTtaaa                                                          >  2:153006/1‑141 (MQ=255)
                                                                               cTTAATATAACAAAAACCACACATCCCCGGAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATATTAGTGCAAGCACCTAAATAATtaaat                                                         >  2:31230/1‑141 (MQ=255)
                                                                                 tAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATtaaataa                                                       <  2:303670/141‑1 (MQ=255)
                                                                                  aaTATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATtaaataaa                                                      >  1:55380/1‑141 (MQ=255)
                                                                                    tataACAAAAACCCCAACTACTGGTAATAGTCGGTGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATg                                                    <  1:88457/141‑1 (MQ=255)
                                                                                           aaaaCCCCAACTACTGGTAATAGGCGGGGTTTGGTAATAAAACATTTAGAAACTGTTTCTGTATATAATTATCG‑ATACTTGTATTATATAATGAATAGTATCTTAGTGCAAGCACCTAAATGATTAACTAAATGTagcgct                                             >  2:38970/1‑136 (MQ=255)
                                                                                               ccccAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTCTTATATGATGAATAATATCTTAGTGCAAGACCATCAAACGTGAAATACATGTCAAGCgaaat                                         >  1:286056/1‑141 (MQ=255)
                                                                                                cccAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaata                                        <  1:209986/141‑1 (MQ=255)
                                                                                                  cAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGGTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaataaa                                      <  1:293642/141‑1 (MQ=255)
                                                                                                   aaCTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATaaaa                                     >  2:325074/1‑141 (MQ=255)
                                                                                                    actactGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATaaaaa                                    <  1:132050/141‑1 (MQ=255)
                                                                                                                   cGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCGTTATATAAATGTAAAGCTAAATAAAAACGTTTTATTACctct                     >  1:14512/1‑141 (MQ=255)
                                                                                                                    gttgTTTGTGAAAAAAACTTTTAGAAACTGTTTA‑TTATAAAATTTTCGAATAC‑TGTAATAAATTAATAAAAATATCCTAATGCCAACCACTAAATCAATAAATAAAATTAAAGCTAAATAAAAACGTTTTATTACCTCTTa                   <  2:186910/138‑1 (MQ=255)
                                                                                                                     gggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACGTAAATCATTAAATAAATGTAAAGCGAAATGAAAACGTTTTATTAcaactga                   >  1:20229/1‑135 (MQ=255)
                                                                                                                         ttGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCaa               >  1:380054/1‑141 (MQ=255)
                                                                                                                         ttGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCaa               >  1:146146/1‑141 (MQ=255)
                                                                                                                         ttGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCaa               <  2:8513/141‑1 (MQ=255)
                                                                                                                           ggTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAAc             >  2:403007/1‑141 (MQ=255)
                                                                                                                                   aaCGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAatat     >  2:123343/1‑141 (MQ=255)
                                                                                                                                     cGTTTAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACAATATTGTACCTCTTACCAAACTAAAATATgg   >  2:276094/1‑141 (MQ=255)
                                                                                                                                      gtatAGAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATCTCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCACAGTAAAAGATGGa  >  2:340637/4‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                        
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCG‑ATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGA  >  CP000731/1‑216

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: ‑