Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	499,203	A→G	100%	intergenic (+47/‑249)	uhpA → / → PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	499,203	0	A	G	100.0%	112.0 / ‑6.8	34	intergenic (+47/‑249)	uhpA/PP_0411	two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (6/27);  minor base T (0/1);  total (6/28)
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.

CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAACAAAT  >  NC_002947/499057‑499348                                                                                                                                                   |                                                                                                                                                  cAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg                                                                                                                                                 <  1:408570/149‑1 (MQ=255) cAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg                                                                                                                                                 >  4:367851/1‑149 (MQ=255) cAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGATGGTGAAGTACACCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg                                                                                                                                                 >  5:78433/1‑149 (MQ=255)      ccATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGc                                                                                                                                            <  6:205400/149‑1 (MQ=255)       cATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGcc                                                                                                                                           >  4:335948/1‑149 (MQ=255)           aGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACACCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCcgcg                                                                                                                                       <  6:78433/149‑1 (MQ=255)            gCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCcgctc                                                                                                                                      <  5:177519/149‑3 (MQ=255)             cACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGaa                                                                                                                                     <  7:123689/149‑1 (MQ=255)             cACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGaa                                                                                                                                     <  4:57386/149‑1 (MQ=255)              aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAAc                                                                                                                                    <  2:229644/149‑1 (MQ=255)               cccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg                                                                                                                                                 >  6:158375/1‑135 (MQ=255)               cccACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACg                                                                                                                                   <  2:197479/149‑1 (MQ=255)                  acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggc                                                                                                                                <  3:247664/149‑1 (MQ=255)                      ggCACGCCTGATGCAGAAGATGAAAGTGAACTGGCGGGCGGAGGTGGCGATGTACGGCATGGAGCAGAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAAGGggcctgg                                                                                                                            <  2:87888/149‑1 (MQ=255)                       gCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggcctggc                                                                                                                           <  4:43065/149‑1 (MQ=255)                             cTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCctgctg                                                                                                                     <  7:127721/149‑1 (MQ=255)                                aTGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAATGGGCCTGGCCTGCTGa                                                                                                                    <  2:41996/147‑1 (MQ=255)                                 tGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGAtct                                                                                                                 <  3:335948/149‑1 (MQ=255)                                    aGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTa                                                                                                              <  5:241006/149‑1 (MQ=255)                                      aaGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATg                                                                                                            <  7:364394/149‑1 (MQ=255)                                       atttGAAAGTGAACTCGCTGGCTGAGCTTGTGAAGTTCGCCATGGAGCACTTGGTGATCTGATTGCGAGATACGGGTGGCCGATACTTGCCGAAGCCTATGTTGGAGGTGGCATGCCCGCGTACGGTCCTTGCGTGCTTATCTCTATgg                                                                                                           <  6:97667/147‑1 (MQ=255)                                       aGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgg                                                                                                           <  3:367851/149‑1 (MQ=255)                                         ttGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCt                                                                                                         >  1:260358/1‑149 (MQ=255)                                             acgggAACTCGCTGGCGCCGCTGGGGAAGTACGCCAGGGAGCACAACCTCAGCTCATTGCGCCATACGGGGCCCCGAAACTTGCCCAAGCCTATGGGGCAGCGGGCATGCCCGCTAACGGGCCTGGCCTGCTGATCTCTATGGCTGAg                                                                                                      <  2:217008/144‑1 (MQ=255)                                               gcgcaCTCGCTGGCGGAGCGGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGCGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCg                                                                                                   <  8:348397/145‑1 (MQ=255)                                                tGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCgg                                                                                                  <  4:305295/149‑1 (MQ=255)                                                           gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCTACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                       <  7:234500/149‑1 (MQ=255)                                                           gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCGCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTcgc                                                                                         <  8:364242/147‑1 (MQ=255)                                                           gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                       <  2:260358/149‑1 (MQ=255)                                                           gCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                       <  1:415585/149‑1 (MQ=255)                                                                gCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAt                                                                                   <  6:37844/148‑1 (MQ=255)                                                                 cTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGc                                                                                 <  5:237710/149‑1 (MQ=255)                                                                                aTGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                       >  6:118035/1‑128 (MQ=255)                                                                                aTGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCgg                                                                                       <  5:118035/128‑1 (MQ=255)                                                                                                                                               gAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCa                                            >  6:336355/1‑108 (MQ=255)                                                                                                                                               gAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCa                                            <  5:336355/108‑1 (MQ=255)                                                                                                                                               gAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAACaaa   >  3:70425/1‑149 (MQ=255)                                                                                                                                                aGCGGGCAAGCCCGCGAACCGGCCAGGCCAGCGGATCTAAATGGCGGAGCCGGCCTCATAGCGGGCATGCCCGCTCCCACACGTTTAGTGGTTGGCTAGCAACGGCATTGCAAAACCGCCAACCATGTATGGGGATACCGA‑AACaaaa  >  4:220293/1‑147 (MQ=255)                                                                                                                                                   |                                                                                                                                                  CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCCTTGTAGGGCGATCCCTACAACAAAT  >  NC_002947/499057‑499348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑