Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,549,188	A→G	10.2%	intergenic (+60/‑76)	pydB → / → pydX	bifunctional D‑hydantoinase/dihydropyrimidinase/NADP‑dependent dihydropyrimidine dehydrogenase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,549,188	0	A	G	10.2%	128.8 / 6.0	49	intergenic (+60/‑76)	pydB/pydX	bifunctional D‑hydantoinase/dihydropyrimidinase/NADP‑dependent dihydropyrimidine dehydrogenase subunit
Reads supporting (aligned to +/- strand):  ref base A (22/22);  new base G (2/3);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-01

AACGGCCGGCGTACCCGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGACCAGTTGGCCGAGCGCTT  >  NC_002947/4549049‑4549328                                                                                                                                             |                                                                                                                                              aaCGGCCGGCGTACCCGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCtgtg                                                                                                                                      <  3:211870/149‑1 (MQ=255)       cggcGTACCCGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAGGCGATCGCGGTC‑CTTGTGGGAGCg                                                                                                                                <  6:194059/149‑1 (MQ=38)           gTACCCGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGccc                                                                                                                            <  3:186470/149‑1 (MQ=255)               ccGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAg                                                                                                                         >  7:194500/1‑148 (MQ=255)                      tgtATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGAcc                                                                                                                 <  4:57697/149‑1 (MQ=255)                          tGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCaa                                                                                                             >  8:101980/1‑149 (MQ=255)                                 cTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGt                                                                                                      >  8:226274/1‑149 (MQ=255)                                    gggCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGc                                                                                                   <  2:31264/149‑1 (MQ=255)                                     ggCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGcc                                                                                                  >  8:148970/1‑149 (MQ=255)                                        gcCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGc                                                                                               <  7:80924/149‑1 (MQ=255)                                          cGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCAc                                                                                             >  2:197977/1‑149 (MQ=255)                                             gCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCa                                                                                           >  2:135944/1‑148 (MQ=255)                                              ccGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAGGCGATCGCGGTC‑CTTGTGGGAGCGGc                                                                                                                              <  7:205949/112‑1 (MQ=25)                                              ccGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAGGCGATCGCGGTC‑CTTGTGGGAGCGGc                                                                                                                              >  8:205949/1‑112 (MQ=25)                                                        gCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATAACTGTCGCCTGCACCAAAAAAAATa                                                                                  >  6:164671/1‑146 (MQ=255)                                                           gCCGATCCCGGTTCCGCGCTGACGTCATTGGGGCTGCGGTGCAGCCCAGCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAgg                                                                            <  4:169720/149‑1 (MQ=39)                                                              gATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTa                                                                         <  7:101980/149‑1 (MQ=255)                                                                tGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATa                                                                                  <  2:204009/138‑1 (MQ=255)                                                                tGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATa                                                                                  >  1:204009/1‑138 (MQ=255)                                                                   cTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATagaga                                                                              >  5:245123/1‑139 (MQ=255)                                                                   cTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATagaga                                                                              <  6:245123/139‑1 (MQ=255)                                                                         cgcgCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGAc                                                              <  5:164671/148‑1 (MQ=255)                                                                         cgcgCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGATAC‑AACCGTGAc                                                              >  6:213843/1‑148 (MQ=255)                                                                            gcTGAAGTCATTGGGGCTGCTGTGCAGCCAATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTTTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAAc                                                          <  1:124196/149‑1 (MQ=255)                                                                              tGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCAGTCGCCTGCACCAAAAAAAATATAGAGGCTAC‑AAACGTGACCAACGc                                                        >  8:56695/1‑149 (MQ=255)                                                                               gAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATag                                                                                 <  8:60622/124‑1 (MQ=255)                                                                                aaGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGccc                                                      >  6:203332/1‑149 (MQ=255)                                                                                 aGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCt                                                     <  5:249271/149‑1 (MQ=255)                                                                                    cATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCCCCAAAAAAAATAGAGAGGCTAC‑AACCGTGCCCAACGCCCTGac                                                  >  3:22860/1‑148 (MQ=255)                                                                                     aTTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATa                                                                                  <  7:97981/117‑1 (MQ=255)                                                                                     aTTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATa                                                                                  >  8:97981/1‑117 (MQ=255)                                                                                     aTTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGa                                                   <  7:148970/147‑1 (MQ=255)                                                                                     aTTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAAc                                                 >  2:192198/1‑149 (MQ=255)                                                                                         gtgctgctGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCAt                                              <  7:56695/146‑1 (MQ=255)                                                                                          ggCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCAttt                                            <  1:197977/149‑1 (MQ=255)                                                                                                   gCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACC‑AAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGTCGCGcccc                                  >  4:251810/1‑149 (MQ=255)                                                                                                       cccATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACC‑AAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGTCGCGCCCCCggg                              <  3:251810/149‑1 (MQ=255)                                                                                                          aTCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGcc                            >  6:171349/1‑149 (MQ=255)                                                                                                           tCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTTGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGATCCATTTGCCGCGCCCCCGGGCCg                           <  7:161928/149‑1 (MQ=255)                                                                                                             gcgACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCgg                          <  7:226274/148‑1 (MQ=255)                                                                                                              cgACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTACAAACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGgc                         <  1:192198/149‑1 (MQ=255)                                                                                                                    aaGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGAc                   >  3:97561/1‑148 (MQ=255)                                                                                                                       gCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGACCAGt               <  1:135944/149‑1 (MQ=255)                                                                                                                          gCTCCCACAGGCGATCGCGGTC‑CTTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGAc                   <  7:43984/142‑1 (MQ=38)                                                                                                                          gCTCCCACAGGCGATCGCGGTC‑CTTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGAc                   >  8:43984/1‑142 (MQ=38)                                                                                                                             cccACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGACCAGTTGGcc          >  4:227274/1‑148 (MQ=255)                                                                                                                                acaAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGCCCAGTTGGCCGAgc      >  4:5855/1‑149 (MQ=255)                                                                                                                                    g‑gACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGACCAGTTGGCCGAGCGCtt  >  4:25243/1‑149 (MQ=255)                                                                                                                                      gACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑ACCCGTGACCAACGCCCTGACCCATTTGCCGCGCCCCCGGGCCGGCGCCGCCCAGTTGGCCGAGCGCtt  >  7:239487/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                              AACGGCCGGCGTACCCGGCGGTGTATGAGGTGCTGGGGCGCCGGGCCGAGCATCAGCGGCCGATGCCTGTTCCGCGCTGAAGTCATTGGGGCTGCTGTGCAGCCCATCGCGACGCAAGGCCGCTCCCACAAG‑GACCGCGATCGCCTGTGGGAGCGGCCCCAGAATCGACCGCAATACCTGTCGCCTGCACCAAAAAAAATAGAGAGGCTAC‑AACCGTGACCAACGCCCTGAACCATTTGCCGCGCCCCCGGGCCGGCGCCGACCAGTTGGCCGAGCGCTT  >  NC_002947/4549049‑4549328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑