Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,605,384 T→C pseudogene (767/987 nt) dgcF ← GGDEF domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,605,3840TC90.3% 76.6 / 2.6 31pseudogene (767/987 nt)dgcFGGDEF domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base C (12/16);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 5.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.70e-01

GACCATCAATTTATTAAAGTCATCGGTCAGCGTTAGGTACGATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTTCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAACACGCTTAA  >  NZ_CP009273/1605248‑1605511
                                                                                                                                        |                                                                                                                               
gACCATCAATTTATTAAAGTCATCGGTCAGCGTTAGGTACGATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTccc                                                                                                                               >  1:11535/1‑139 (MQ=255)
         tttATAAAAGTCACCGGTCGGCGTTAGGTACGATGCGCGCCCACTCCCGCCGCAAATATTTCCCGTGAGAAAAAGCGTTTTTTTTTGCCAGGTGAATGTTTGCAGTCCACCGCCTTTACGGTTTTTTCCCGCCATTAGc                                                                                                                      <  2:689359/139‑1 (MQ=255)
          ttataaAAGTCATGGGACGGCGTTAGGTCCGATGCGCCCCCCCTCCCGCCGCCAATACTTCCCGGGAGAAAAAGCTTTTTTTGTTGCCAGGTGAATGTTTGCAGTTCACCGCTTTTACGTTTTTTCCCCGCCATTAGc                                                                                                                      <  2:1028930/138‑1 (MQ=255)
             ttaAAGCCATCGGTCAGCGTTAGGTACGAGGCGCGCCCCCTCCCGACGCCAATACTTCCCGTGAGATAAAGCGTTTTTTGTTCCCAGGTGAAGGTTTGCAGTTCAACGCTTTTAGGGATTTTTCCCGCCATTAGCAGa                                                                                                                   <  2:440547/138‑1 (MQ=255)
               aaaGTCACCGGTCGGCGTTAGGTCCGATGCGCGCCCACTCCCGACGCCAATACTTACCGTGAGATAAAGCTTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCACCGCCTTTACGGATTTTTCCCGCCATTAGCAGAcc                                                                                                                 <  2:642766/138‑1 (MQ=255)
                   tCATCGGTCAGCGTTAGGTACGATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGa                                                                                                            >  2:74566/1‑139 (MQ=255)
                     aTCGGTCAGCGTTAGGTACGATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGa                                                                                                            >  1:1143337/1‑137 (MQ=255)
                              cGTTAGGTCCGATGCGCCCCCCCTCCCGACGCCAATCCTTACCGTGAAATAAAGCTTTTTTTGTTGCCGGGTGAATGGTTGCAGTCCACCGCTTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCAcc                                                                                                 <  2:68705/139‑1 (MQ=255)
                                        gATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTTCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTg                                                                                       >  2:402865/1‑139 (MQ=255)
                                        gATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTg                                                                                       >  2:471197/1‑139 (MQ=255)
                                        gATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTg                                                                                       >  1:822570/1‑139 (MQ=255)
                                                   aCTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAAt                                                                            >  1:723132/1‑139 (MQ=255)
                                                         gccGCAAATCCTTCCCGTGAGATAAAGCTTTTTTTGTTGCCGGGTGAATGTTTGCATTTCACCGCCTTTACGGTTTTTCCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTcg                                                                      <  2:723132/137‑1 (MQ=255)
                                                           cGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTcgcc                                                                    >  2:51608/1‑139 (MQ=255)
                                                               aaTACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGa                                                                                                            <  1:236424/95‑1 (MQ=255)
                                                               aaTACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGa                                                                                                            >  2:236424/1‑95 (MQ=255)
                                                                      aCCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTcgcg                                                         >  2:936880/1‑139 (MQ=255)
                                                                      aCCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTcgcg                                                         >  1:1204849/1‑139 (MQ=255)
                                                                            agaTAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTTCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGccac                                                     >  2:1243033/1‑137 (MQ=255)
                                                                            agaTAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGccac                                                     >  1:410804/1‑137 (MQ=255)
                                                                                 aggCGTTTTTTTTTCCAGGGTAAATGTTGGCATTCCACCTCCTTTAGGGTTTTTCCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGcccc                                              <  2:410804/137‑1 (MQ=255)
                                                                                             ttcccAGGTGAATGGTTGCATCCAAACCCCTTAACGGATTTTCCCCGCCATTAGCAGACCAGCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTGCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCTACa                                  <  2:181060/136‑1 (MQ=255)
                                                                                                 cggttaaaTGGTTGCAGTTCACCGCTTTACCGGTTTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAAtct                              <  1:359280/133‑1 (MQ=255)
                                                                                                           gTTGCAGTTCAACGCCTTTACGGATTTTTTCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATg                    <  1:1243033/139‑1 (MQ=255)
                                                                                                              gCAGTTCAACGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCg                 >  1:76897/1‑139 (MQ=255)
                                                                                                                     aaCGCCTTTACGTATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAac          <  2:76897/139‑1 (MQ=255)
                                                                                                                     aaCGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAac          <  1:936880/139‑1 (MQ=255)
                                                                                                                       cGCTTTTAGGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAAtctt                             <  1:235920/118‑1 (MQ=255)
                                                                                                                       cGCCTTTACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAAtctt                             >  2:235920/1‑118 (MQ=255)
                                                                                                                            ttccGGTTTTTCCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAACACGCt     <  2:1143337/134‑1 (MQ=255)
                                                                                                                             tACGGATTTTTCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAACACGCtt    <  2:690953/137‑1 (MQ=255)
                                                                                                                              cggtaTTTTCCCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAACACGCTTaa  <  1:611899/134‑1 (MQ=255)
                                                                                                                                    ttttcCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGcccc                                              >  1:396707/1‑88 (MQ=255)
                                                                                                                                    ttttcCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGcccc                                              <  2:396707/88‑1 (MQ=255)
                                                                                                                                        |                                                                                                                               
GACCATCAATTTATTAAAGTCATCGGTCAGCGTTAGGTACGATGCGCGACCACTACCGACGCCAATACTTACCGTGAGATAAAGCGTTTTTTGTTGCCAGGTGAATGGTTGCAGTTCAACGCCTTTACGGATTTTTTCCGCCATTAGCAGACCATCGACAGGATTCACCGACGGCACTGCAACAGCAAATTCTTCGCCGCCCATTCGCGCCACCAGCCCCTTATCACCGACAATCTTCTGAATATGCCGGGCAAACACGCTTAA  >  NZ_CP009273/1605248‑1605511

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑