Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,398,903	C→G	10.9%	intergenic (+123/‑119)	aroQ‑III → / → PP_3004	type II 3‑dehydroquinate dehydratase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,398,903	0	C	G	10.9%	132.3 / 6.6	46	intergenic (+123/‑119)	aroQ‑III/PP_3004	type II 3‑dehydroquinate dehydratase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/18);  new base G (3/2);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

GGCGATGAGCATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGATCAGTCAA  >  NC_002947/3398762‑3399048                                                                                                                                              |                                                                                                                                                     ggcgATGAGCATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCatggatg                                                                                                                                               <  1:207495/149‑1 (MQ=255)     aTGAGCATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCATGctggatgggta                                                                                                                                           <  6:218122/149‑4 (MQ=255)     aTGAGCATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCATGctggatgggta                                                                                                                                           <  5:27237/149‑4 (MQ=255)          cATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCa                                                                                                                                       <  8:308540/148‑1 (MQ=255)                    gCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTc                                                                                                                            >  4:285159/1‑149 (MQ=255)                             aGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGc                                                                                                                   <  3:115884/149‑1 (MQ=255)                                  tCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAg                                                                                                               >  5:293006/1‑148 (MQ=255)                                   cGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTa                                                                                                             <  3:285159/149‑1 (MQ=255)                                    ggATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTAc                                                                                                            >  7:296902/1‑149 (MQ=255)                                          ccGAGCGCGTCTACCCGCGAAGTAGGTGGCGCGGGGAATGCGGCCACGGCGACTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCAGCCTACCCAACCAGCATGGATGAAAACCCAGAAGCGAGTTCCGTGACTGCAAAGTACGGTCCg                                                                                                      >  7:56363/1‑149 (MQ=255)                                                gcgTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTAACCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTc                                                                                                 >  6:370514/1‑148 (MQ=255)                                                  gTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTc‑‑aa                                                                                             >  7:79339/1‑148 (MQ=255)                                                      aCCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGc                                                                                       >  2:242089/1‑149 (MQ=255)                                                         cgcgAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCAc                                                                                    >  8:23890/1‑149 (MQ=255)                                                                cAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTc                                                                             <  8:296902/149‑1 (MQ=255)                                                                   gTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGtt                                                                          >  4:26044/1‑149 (MQ=255)                                                                     ggCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGc                                                                        <  8:79339/149‑1 (MQ=255)                                                                               aTGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAAccc                                                               >  1:150342/1‑148 (MQ=255)                                                                                  cggcgACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACg                                                           >  7:210137/1‑149 (MQ=255)                                                                                              cTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCgg                                                                                <  7:300141/116‑1 (MQ=255)                                                                                              cTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCgg                                                                                >  8:300141/1‑116 (MQ=255)                                                                                              cTGAAGTAACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTcc                                                                                                       <  5:186012/96‑1 (MQ=255)                                                                                              cTGAAGTAACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTcc                                                                                                       >  6:186012/1‑96 (MQ=255)                                                                                                 aaGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCAt                                            <  6:293006/149‑1 (MQ=255)                                                                                                        cGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTgg                                     >  4:367418/1‑149 (MQ=255)                                                                                                         gTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTggg                                    <  3:26044/149‑1 (MQ=255)                                                                                                                  gtggATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAAt                           <  8:210137/149‑1 (MQ=255)                                                                                                                         tctttctgcCTACACTTCCAGCATGGATGGAAAGCAATTAGCTACTTCCGTGACTGCATAGTACGTTCCGCCTTA‑‑AA‑CAAGCAACCCGGTTCTTTGCATCCAACCACACGGACCGGGGCTCTCATGAACTGGGAGGTCGAATGTACGt                     <  1:46480/143‑1 (MQ=255)                                                                                                                         tCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTc                    >  3:66226/1‑149 (MQ=255)                                                                                                                           gTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGGCGTCGc                  >  6:25631/1‑149 (MQ=255)                                                                                                                            tgctgcCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCt                 <  4:66226/149‑1 (MQ=255)                                                                                                                             gctgcCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTa                >  4:23424/1‑149 (MQ=255)                                                                                                                               tggctttccatccatGCTGGATGGGTAGGCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTAc               >  7:88780/8‑148 (MQ=255)                                                                                                                               tgcCTACCCATCCAGCATGGATGTAAAGCCAGTAGCGAATTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCAACACGGTTCGTTGCCTCCAACACCACGGACCGGGGCTCTCATGACCTGCGAGGACGAATGGACGTCTCTAc               >  7:334910/1‑148 (MQ=255)                                                                                                                               tgcCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTgg                                     >  3:262680/1‑126 (MQ=255)                                                                                                                               tgcCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTgg                                     <  4:262680/126‑1 (MQ=255)                                                                                                                               tagctttccatccatGCTGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTCAGAAGCAAGCCACCCGGTTCGTTGCCTCCAACCCCACCGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGc                  >  1:114955/8‑148 (MQ=255)                                                                                                                                 gctttccatccatGCTGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAAc            >  3:191663/6‑149 (MQ=255)                                                                                                                                    aCCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGAt         >  2:326778/1‑149 (MQ=255)                                                                                                                                    aCCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGAt         <  3:23424/149‑1 (MQ=255)                                                                                                                                    aCCCATCCAGCATGGAAGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGAt         >  3:97831/1‑149 (MQ=255)                                                                                                                                        aTCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAAc            <  2:219424/142‑1 (MQ=255)                                                                                                                                        aTCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAAc            >  1:219424/1‑142 (MQ=255)                                                                                                                                         tCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGATCAGt     >  1:239710/1‑148 (MQ=255)                                                                                                                                         tCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGATCAGTc    <  7:23890/149‑1 (MQ=255)                                                                                                                                           cAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGATCAGTcaa  <  2:150342/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                     GGCGATGAGCATGGTCTGAGCAGGGCGCAGGGGTCGGATCTCCGAGCGCGTCTACCCGCGAAGCAGGTGGCGCGGGGCATGCGGCGACGGCGCCTGAAGTGACCGTAGGTGTGGTGGATGTCGTGCTGCCTACCCATCCAGCATGGATGGAAAGCCAGTAGCGACTTCCGTGACTGCATAGTACGGTCCGCCTTC‑‑AA‑CAAGCCACCCGGTTCGTTGCCTCCAACCCCACGGACCGGGGCTCTCATGACCTGGGAGGTCGAATGGACGTCGCTACAACGATCAGTCAA  >  NC_002947/3398762‑3399048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑