Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,953,269	C→A	10.9%	R388L (CGG→CTG)	PP_4363 ←	two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,953,269	0	C	A	10.9%	123.1 / 4.4	45	R388L (CGG→CTG)	PP_4363	two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base C (18/22);  new base A (3/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 6.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

GCAGGCCATGAATTTCCTGCAACAACTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTGTACGCC  >  NC_002947/4953123‑4953417                                                                                                                                                    |                                                                                                                                                     gcAGGCCATGAATTTCCTGCAACAACTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGc                                                                                                                                                    <  2:80890/149‑1 (MQ=255)       cATGAATTTCCTGCAACAACTGCACAAGGTACGGCACAGGGTTGAAGAGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGAAAAGTCCAGCGGGCT‑GGAGCGGACACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCg                                                                                                                                              >  1:244745/1‑149 (MQ=255)        aTGAATTTCCTGCAACAACTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCgg                                                                                                                                             <  4:69692/149‑1 (MQ=255)                ccTGCAACAACTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGaa                                                                                                                                      >  1:16844/1‑148 (MQ=255)                    caacaaCTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGc                                                                                                                                 <  5:278304/149‑1 (MQ=255)                          cTGCACCAGGTACGGAACAGGGTTGTAGCGTTTCAGGCTTTCGCCACGCACCTCGATGCTCAGCGACCAGTCCAGAGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGTGCCGCCACCAGCTCCTCGGCAGTGAACATGCGAatat                                                                                                                           <  2:244745/149‑1 (MQ=255)                             cACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCg                                                                                                                         <  4:38345/148‑1 (MQ=255)                             cACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCCGGGT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCg                                                                                                                         <  5:336987/148‑1 (MQ=255)                              aCCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGca                                                                                                                       <  7:245972/149‑1 (MQ=255)                                  gttACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGAGCTGTCTAGCTGGCT‑GGAGCGGCCACTATCTGAGTATATCCTCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAg                                                                                                                   <  7:272687/147‑1 (MQ=255)                                       ggCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGAt                                                                                                              <  1:298041/149‑1 (MQ=255)                                              ggTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATcg                                                                                                       >  1:45955/1‑149 (MQ=255)                                                    aGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCTAGGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTgg                                                                                                  >  1:263395/1‑149 (MQ=255)                                                       gTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGc                                                                                              <  5:322404/149‑1 (MQ=255)                                                        tttCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGcc                                                                                             >  2:145978/1‑149 (MQ=255)                                                        tttCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGcc                                                                                             <  4:300138/149‑1 (MQ=255)                                                           cAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATg                                                                                                                                  >  8:268509/1‑109 (MQ=255)                                                           cAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATg                                                                                                                                  <  7:268509/109‑1 (MQ=255)                                                             ggCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCccacc                                                                                         >  2:330015/1‑148 (MQ=255)                                                              gCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCccacca                                                                                        >  1:204476/1‑148 (MQ=255)                                                                   cGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACg                                                                                   <  1:145978/148‑1 (MQ=255)                                                                         gCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCcca                                                                                           <  6:5593/134‑1 (MQ=255)                                                                         gCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTc                                                                                >  3:178821/1‑145 (MQ=255)                                                                         gCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTc                                                                                <  4:178821/145‑1 (MQ=255)                                                                           aCCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGc                                                                          <  4:58093/149‑1 (MQ=255)                                                                                 aaGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCAt                                                                    <  3:229179/149‑1 (MQ=255)                                                                                  aGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATc                                                                   <  1:330015/149‑1 (MQ=255)                                                                                     tCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCAACGTGGACGCCAACAGATAAAAAAAAAAGAACATGCGAAAATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAg                                                                 >  2:39962/1‑148 (MQ=255)                                                                                        gCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCAACGTGGACGCCAAAACATAAAAAAAAAAAAAAATGCGAATATAGCACAAGCTGATGTCATCGCGTGGCTGCGCACAAAAACGCTACAGGGCCAGCATCAGCTCa                                                             >  2:22773/1‑149 (MQ=255)                                                                                           aCCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGTGGACGCCAACAAATAATATAAAGTGAACATGCGAATATCGCACAAGCTGATGTCATCTCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATc                                                           >  4:285800/1‑148 (MQ=255)                                                                                              aGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCATCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCCGCTCATCGaa                                                        >  6:68092/1‑148 (MQ=255)                                                                                                  cAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGATAATCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACt                                                   >  6:46878/1‑149 (MQ=255)                                                                                                                 ggCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCgg                                     <  2:204476/149‑1 (MQ=255)                                                                                                                   ccACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTAGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGtt                                   <  2:45955/149‑1 (MQ=255)                                                                                                                         tCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGaac                                                       >  7:46657/1‑123 (MQ=255)                                                                                                                         tCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGaac                                                       <  8:46657/123‑1 (MQ=255)                                                                                                                           agagTAGATCATCGGGGCCGCCACCCGCTAATCGGCACTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCa                           >  4:80445/1‑149 (MQ=255)                                                                                                                                 gATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCg                     >  7:309455/1‑149 (MQ=255)                                                                                                                                        ggggCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAg              <  2:16844/149‑1 (MQ=255)                                                                                                                                         gggCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAgg             >  8:238861/1‑149 (MQ=255)                                                                                                                                          ggCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGgc            >  4:254877/1‑149 (MQ=255)                                                                                                                                              gccACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTg        >  4:187151/1‑149 (MQ=255)                                                                                                                                              gccACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTg        >  6:57093/1‑149 (MQ=255)                                                                                                                                               ccACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTGt       <  7:238861/149‑1 (MQ=255)                                                                                                                                                 aCCAGCTACTCGGCAGTGAACATGCGAATCTCGCACACGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTGTAc     <  8:309455/149‑1 (MQ=255)                                                                                                                                                    cGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTGTACGcc  <  2:263395/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GCAGGCCATGAATTTCCTGCAACAACTGCACCAGGTACGGCACAGGGTTGAAGCGTTTCAGGCTTTCGCCACGCACCTCGAAGCTCAGCGACCAGTCCAGCGGGCT‑GGAGCGGCCACTATCAGAGTAGATCATCGGGGCCGCCACCCGCTCCTCGGCAGTGAACATGCGAATATCGCACAAGCTGATGTCATCGCGTGGCTGCCCACCAAAACGCTCCAGGGCCAGCATCAGCTCATCGAACAACTTCACCGGGTCGCGGTTGTCGGCCAGCACCGCTCGCAGGCGCTGTACGCC  >  NC_002947/4953123‑4953417

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: ‑