Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,371,693 A→G I349T (ATC→ACC)  menD ← 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,371,6930AG97.5% 136.3 / ‑3.7 41I349T (ATC→ACC) menD2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (21/18);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.20e-01

CCACCAGGCTGTTACCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGATTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATCAACAATCCAGTACTCTT  >  NZ_CP009273/2371559‑2371828
                                                                                                                                      |                                                                                                                                       
ccaccaGGCTGTTACCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGttt                                                                                                                                      >  2:365096/1‑138 (MQ=255)
ccaccaGGCTGTTACCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGttt                                                                                                                                      >  1:650635/1‑138 (MQ=255)
  accaGGCTGTTACCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGTTTCGCCAAACGCATCCGGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCaa                                                                                                                                   <  2:311424/139‑1 (MQ=255)
             aCCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGc                                                                                                                        >  2:557625/1‑139 (MQ=255)
                 acaaacaaTTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGc                                                                                                                    >  2:971811/1‑139 (MQ=255)
                  caaccaaTTGCCCCTGTTCAGGCAGATAGCCGCGGATGCGATGCGCCAGTTGCGCTTCGCAAACCGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCg                                                                                                                   <  2:823812/139‑1 (MQ=255)
                  caaacaaTTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCg                                                                                                                   >  2:641204/1‑139 (MQ=255)
                     acaaTTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGttt                                                                                                                >  2:218527/1‑139 (MQ=255)
                            ccccTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGcc                                                                                                         >  1:1228522/1‑139 (MQ=255)
                                          gATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTccag                                                                                           >  2:880950/1‑139 (MQ=255)
                                          gATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTccag                                                                                           >  2:973688/1‑139 (MQ=255)
                                            tAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTccagc                                                                                          >  1:306003/1‑138 (MQ=255)
                                                 gCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCg                                                                                    >  2:1238734/1‑139 (MQ=255)
                                                               ccAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGa                                                                                                      <  1:491031/107‑1 (MQ=255)
                                                               ccAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGa                                                                                                      >  2:491031/1‑107 (MQ=255)
                                                               ccAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAAt                                                                      >  2:278395/1‑139 (MQ=255)
                                                                       gcTTCGCCAAACGCACCCCGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGAc                                                              <  2:91387/139‑1 (MQ=255)
                                                                               aaccGCATCCCGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGa                                                      <  1:38525/136‑1 (MQ=255)
                                                                                 aCGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATg                                                    <  1:365096/139‑1 (MQ=255)
                                                                                     aTCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGgtgt                                                >  1:884881/1‑139 (MQ=255)
                                                                                     aTCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGgtgt                                                >  2:1213823/1‑139 (MQ=255)
                                                                                       cACGGGGGGCAATAACCGCCAGCATTGCCTGTGAATAAAGGAGAGGGTGGGAAAAGAACAAGGGCGGGCGGGTTGCTGCCGGATGCAGCTCCAGCCAGTCGGCTAGAATTGCAAGGAAGAGACGGCCGCGAGGGTGTGc                                              <  2:732645/139‑1 (MQ=255)
                                                                                             gggCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCa                                                                                 <  1:478652/98‑1 (MQ=255)
                                                                                             gggCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCa                                                                                 >  2:478652/1‑98 (MQ=255)
                                                                                                 aaTAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGt                                    <  1:1213823/139‑1 (MQ=255)
                                                                                                   tAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCg                                  <  1:386168/139‑1 (MQ=255)
                                                                                                   tAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCg                                  <  1:557625/139‑1 (MQ=255)
                                                                                                     aCCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGcc                                <  2:1074035/139‑1 (MQ=255)
                                                                                                         ccTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATg                                                                                                    >  2:717655/1‑67 (MQ=255)
                                                                                                         ccTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATg                                                                                                    <  1:717655/67‑1 (MQ=255)
                                                                                                         ccTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCtt                             >  1:778373/1‑138 (MQ=255)
                                                                                                          cTGCATTGCCTGTTCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCa                           <  1:851421/139‑1 (MQ=255)
                                                                                                              aTTGCCTGTTCCGCCAGGCGCGGGATTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGt                       <  1:988627/139‑1 (MQ=255)
                                                                                                                      ttCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATcaa                 <  2:1079865/137‑1 (MQ=255)
                                                                                                                      ttCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATcaa                 <  1:454282/137‑1 (MQ=255)
                                                                                                                      ttCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATcaa                 <  1:218527/137‑1 (MQ=255)
                                                                                                                       tCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCg                                                                >  1:97993/1‑89 (MQ=255)
                                                                                                                       tCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCg                                                                <  2:97993/89‑1 (MQ=255)
                                                                                                                       tCCGCCAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATcaacaa              >  2:639960/1‑139 (MQ=255)
                                                                                                                           ccAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCa                           >  1:882909/1‑122 (MQ=255)
                                                                                                                           ccAGGCGCGGGGTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCa                           <  2:882909/122‑1 (MQ=255)
                                                                                                                                   ggggTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATCAACAATCCAGTACtctt  <  1:1101331/139‑1 (MQ=255)
                                                                                                                                   ggggTTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATCAACAATCCAGTACtctt  <  1:971811/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                       
CCACCAGGCTGTTACCAACAAACAATTGCCCCTGTTCAGGCAGATAGTCGCAGATGCGATGCGCCAGTTGCGCTTCGCCAAACGCATCACGGCGGGCAATAACCGCCTGCATTGCCTGTTCCGCCAGGCGCGGGATTTCAACGCACCAGGGCTGGCGTTTTTCTGCCGGATGCAGCTCCAGCCAGTCGGCAATATTGGCAATTAAGCGACGTCCGCGATGGTGTGCCGGATCAAGTCGCCCTTCAATGTCATCAACAATCCAGTACTCTT  >  NZ_CP009273/2371559‑2371828

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑