Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,021,361	C→T	11.1%	intergenic (+5/+3)	PP_3546 → / ← PP_3547	two‑component system sensor histidine kinase/response regulator/NAD(P)‑binding oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,021,361	0	C	T	11.1%	88.9 / 3.2	36	intergenic (+5/+3)	PP_3546/PP_3547	two‑component system sensor histidine kinase/response regulator/NAD(P)‑binding oxidoreductase
Reads supporting (aligned to +/- strand):  ref base C (20/12);  new base T (2/2);  total (22/14)
Fisher's exact test for biased strand distribution p-value = 6.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

GACCTCAAGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGACGCGGTC  >  NC_002947/4021213‑4021507                                                                                                                                                     |                                                                                                                                                    gACCTCAAGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGgc                                                                                                                                                     <  6:131500/149‑1 (MQ=255) gACCTCAAGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGgc                                                                                                                                                     <  7:276475/149‑1 (MQ=255)     tCAAGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGCCGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGgcggt                                                                                                                                                  >  6:327094/1‑146 (MQ=255)       aaGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCTTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTTACCAAGCCGTTCGAACTGGTTGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCa                                                                                                                                                <  5:327094/148‑1 (MQ=255)       aaGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTc                                                                                                                                                 <  6:109001/147‑1 (MQ=255)                   aTCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCgccgcc                                                                                                                                    >  6:96819/1‑148 (MQ=255)                    tCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCACCCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGCGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCgccgcc                                                                                                                                    >  2:215849/1‑147 (MQ=255)                          gCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑Ga                                                                                                                           >  3:26828/1‑149 (MQ=255)                                           gcgTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGTGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCa                                                                                                          >  3:87236/1‑149 (MQ=255)                                                        gCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGGCGGGCGCTGAGcgcccgtcaag                                                                                                                                    <  5:194958/111‑6 (MQ=255)                                                        gCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGGCGGGCGCTGAGcgcccgtcaag                                                                                                                                    >  6:194958/1‑106 (MQ=255)                                                                  gCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCaa                                                                                   >  5:36480/1‑149 (MQ=255)                                                                   catggTACGTGGGTGTTGACCAAGCCGTTCGAACTGCAAGCACGGGCAGAGCGGGTTCGCGAGCTGCTGTAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAAc                                                                                  <  5:167352/146‑1 (MQ=255)                                                                   cAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAAc                                                                                  >  3:178817/1‑149 (MQ=255)                                                                                    gACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGc                                                                 >  1:156173/1‑149 (MQ=255)                                                                                       cAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGTGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATg                                                                         >  6:26630/1‑138 (MQ=255)                                                                                       cAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGTGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATg                                                                         <  5:26630/138‑1 (MQ=255)                                                                                       cAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGa                                                                                                                        >  2:235275/1‑91 (MQ=255)                                                                                       cAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTCCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGa                                                                                                                        <  1:235275/91‑1 (MQ=255)                                                                                             gTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTc                                                        >  8:106248/1‑149 (MQ=255)                                                                                              gccGAACTGTCAGCACGGGCAGCGCGCGTCCCCCACCTCCTGCACCCTTCCCGGCCGCCCCCCCCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCg                                                       <  6:109306/147‑1 (MQ=255)                                                                                                  aaCTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGaaa                                                                                       <  1:102361/113‑1 (MQ=255)                                                                                                  aaCTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGaaa                                                                                       >  2:102361/1‑113 (MQ=255)                                                                                                       gacgCACTGCCCCAGCGGGTGCCCGAGCGCCTGCAACCTTGACGGCCGCCCCGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGccc                                               <  5:96819/145‑1 (MQ=255)                                                                                                        aaGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGccccc                                             >  4:249523/1‑149 (MQ=255)                                                                                                            aCTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCg                                         >  3:3031/1‑149 (MQ=255)                                                                                                             cTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCgg                                        >  5:306930/1‑149 (MQ=255)                                                                                                                  cgcccGGGTCCGCTAGCGGCTGCAACCTTCACGGGCGCCCCCCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCAt                                   <  7:137432/145‑1 (MQ=255)                                                                                                                   gagCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATg                                  <  3:249523/149‑1 (MQ=255)                                                                                                                    agCGGGTTCGCGAGCTGCTGGAACCTTGACGGGTGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATgg                                 <  4:87236/149‑1 (MQ=255)                                                                                                                              cgAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GAGGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAACCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATACGCAAGcacgg                       >  3:4877/1‑145 (MQ=255)                                                                                                                                      tgGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCt               >  2:189050/1‑149 (MQ=255)                                                                                                                                        taaCCTTGACGGGCGCTATGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGATGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCtt              <  6:306930/147‑1 (MQ=255)                                                                                                                                        gAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGGCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTg             <  1:215849/149‑1 (MQ=255)                                                                                                                                            cTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGa         >  8:219306/1‑149 (MQ=255)                                                                                                                                             ttGACGGGCGCTCAGCGCCCGCCGCCCAGGTCGGATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGa         >  1:211554/1‑149 (MQ=255)                                                                                                                                               ggcGGGCGCTGAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGCGCTTGCTGAcgc      >  2:85776/3‑149 (MQ=255)                                                                                                                                               ggcGGGCGCTGAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGAcgc      >  2:289613/3‑149 (MQ=255)                                                                                                                                                   ggCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGACGCGGTc  >  4:320313/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GACCTCAAGGTGCTGTTGATCACCGGCTACGATGAGAGTGCGGCGTTCAGCGACGGCCAACCGCTGCAAGGTACGTTGGTGTTGACCAAGCCGTTCGAACTGGAAGCACTGGCAGAGCGGGTTCGCGAGCTGCTGGAACCTTGACGGGCGCTCAGCGCCCGCCGCCCAGGTC‑GATGAGGCTGCCGGTGGCATAGGAGGCTTTGTCCGAAAGCAACCAGAGGATGGCCTCGGCCACTTCCTCGGGACGCCCCCCTCGGCCCATGGGCAAGCCAGGTTCGAGCTTGCTGACGCGGTC  >  NC_002947/4021213‑4021507

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: ‑