Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,070,477	C→T	9.9%	intergenic (+45/‑309)	aldB‑II → / → pqqD‑II	aldehyde dehydrogenase/coenzyme PQQ synthesis protein D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,070,477	0	C	T	9.9%	138.4 / 5.1	51	intergenic (+45/‑309)	aldB‑II/pqqD‑II	aldehyde dehydrogenase/coenzyme PQQ synthesis protein D
Reads supporting (aligned to +/- strand):  ref base C (23/22);  new base T (2/3);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.27e-01

AGTCCGGTGTTGGCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAAT  >  NC_002947/3070329‑3070620                                                                                                                                                     |                                                                                                                                                  agTCCGGTGTTGGCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGTGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCAc                                                                                                                                                   <  1:56014/149‑1 (MQ=255) agTCCGGTGTTGGCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCAc                                                                                                                                                   <  2:36618/149‑1 (MQ=255)      ggTGTTGGCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTg                                                                                                                                              >  2:214606/1‑149 (MQ=255)            ggCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTc                                                                                                                                          >  4:196646/1‑147 (MQ=255)                   agaCCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCgg                                                                                                                                 >  1:300472/1‑149 (MQ=255)                    gaCCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGt                                                                                                                                >  6:146733/1‑149 (MQ=255)                    gaCCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGt                                                                                                                                <  4:349711/149‑1 (MQ=255)                     aCCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTg                                                                                                                               <  3:196646/149‑1 (MQ=255)                      cccACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTga                                                                                                                              <  2:68941/149‑1 (MQ=255)                       ccACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTgaa                                                                                                                             >  7:187599/1‑149 (MQ=255)                           aaGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAAc                                                                                                                         <  1:299562/149‑1 (MQ=255)                                gatgCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCtgtg                                                                                                                    >  1:346600/1‑149 (MQ=255)                                 atgCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCTTCACCGGTTCTGGAACCAGCGGTGAACCtgtg                                                                                                                    <  3:236647/148‑1 (MQ=18)                                  tgCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTTAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTgg                                                                                                                   <  8:187599/148‑1 (MQ=255)                                      tGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGggg‑cg                                                                                                             >  6:162918/1‑149 (MQ=255)                                       gACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCTTGACCGGTTCTGGAACCAGCGGTGAACCTGTGGgag‑c                                                                                                              <  7:99361/147‑1 (MQ=18)                                        aCCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTCGCCCGCCCCCACAGGTTCTTCACCGGTTCTGGAACCAGCGGTGAACCTGTGGgag‑c                                                                                                              >  4:56938/1‑146 (MQ=18)                                        aCCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTCGCCCGCCCCCACAGGTTCTTCACCGGTTCTGGAACCAGCGGTGAACCTGTGGgag‑c                                                                                                              <  3:56938/146‑1 (MQ=18)                                           aTTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGa                                                                                                        <  5:39269/149‑1 (MQ=255)                                            ttATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGggg‑cgggc                                                                                                          >  2:209674/1‑146 (MQ=255)                                            ttATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGggg‑cgggc                                                                                                          <  1:209674/146‑1 (MQ=255)                                            ttATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAg                                                                                                       >  6:131377/1‑149 (MQ=255)                                               tCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGc‑c                                                                                                    <  2:310015/148‑1 (MQ=255)                                                   cagACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGGGAGC‑CCGCa                                                                                                >  2:329529/1‑148 (MQ=255)                                                   cagACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCaa                                                                                               <  1:329529/149‑1 (MQ=255)                                                        cAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTggg                                                                                                                  <  6:277585/127‑1 (MQ=255)                                                        cAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTggg                                                                                                                  >  5:277585/1‑127 (MQ=255)                                                        cAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAggg                                                                                          >  4:276654/1‑149 (MQ=255)                                                          aGAACCTGCTGGTGAGCTACGACATCAATCCGCTGCGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGcc                                                                                        <  3:88622/149‑1 (MQ=255)                                                                  ctgGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGGCCGGGCGAGC‑CCGCAAAAGGGCCGGCAcat                                                                                 <  1:214606/149‑1 (MQ=255)                                                                  cgtgTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAACCCGCGTCTCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACGTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCAcat                                                                                 <  4:300144/145‑1 (MQ=255)                                                                         gCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGCTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGc                                                                          >  1:177003/1‑148 (MQ=255)                                                                             cGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTa                                                                       <  5:131377/147‑1 (MQ=255)                                                                                     aTCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCaa                                                             <  5:146733/149‑1 (MQ=255)                                                                                      tCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAAc                                                            <  2:346600/149‑1 (MQ=255)                                                                                            gggCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCAccc                                                      >  5:247220/1‑149 (MQ=255)                                                                                            cggCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTGGCCCGCTCCCACAGGTGCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCAccc                                                      <  6:239827/148‑1 (MQ=255)                                                                                                     ctAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTc                                             >  7:69089/1‑149 (MQ=255)                                                                                                     ctAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTc                                             >  1:258150/1‑149 (MQ=255)                                                                                                        aaCCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTACAACGCTGGTTCCAGAACCGGTGAAGAACCACTGGCGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTCCCCGTACCAACGCACCCCCCAAGCTCGtt                                          >  6:375042/1‑149 (MQ=255)                                                                                                           cgcgTCGCGGCCTTCGCGGGCTTTCCCGCTCCCACAAGTTAACCGCAGGTTACAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAAC‑CCGCAAAACGGCCCGCACATTCATGGCCTACCCCTACCAACGCACCCCCCAACCACCTTcc                                        >  4:15362/1‑148 (MQ=255)                                                                                                              gTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAg                                    >  2:18029/1‑149 (MQ=255)                                                                                                                  cgGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGCTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGc                                <  2:177003/149‑1 (MQ=255)                                                                                                                         cgcgGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAACTAGCATTCg                           <  2:64188/147‑1 (MQ=255)                                                                                                                            gtgattGCCGGCTCCCACAGGTTCACCTCTGGTTCCAGAACCTGTGAAGAACCTTTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCa                      <  3:15362/145‑1 (MQ=255)                                                                                                                            gggCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTc                        >  7:17858/1‑147 (MQ=255)                                                                                                                                      gcccccACAGGTTCTTCACCGGTTCTGGAACCAGCGGTGAACCTGTGGGAG‑CGGGCAAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGccccc            >  7:306134/4‑149 (MQ=21)                                                                                                                                        tCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGt          >  5:222095/1‑149 (MQ=255)                                                                                                                                          ccACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTg         <  1:18029/148‑1 (MQ=255)                                                                                                                                                gTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAAt  >  4:356631/1‑149 (MQ=255)                                                                                                                                                gTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAAt  >  6:245226/1‑149 (MQ=255)                                                                                                                                                 ttCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGCGCCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAAt  >  1:278602/1‑149 (MQ=255)                                                                                                                                                 gacACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCgg                          <  4:292121/122‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  AGTCCGGTGTTGGCCGTGAGACCCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAAT  >  NC_002947/3070329‑3070620

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: ‑