Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,070,499	A→T	10.6%	intergenic (+67/‑287)	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	3,070,499	0	A	T	10.6%	125.4 / 6.4	47	intergenic (+67/‑287)	aldB‑II/pqqD‑II	aldehyde dehydrogenase/coenzyme PQQ synthesis protein D
Reads supporting (aligned to +/- strand):  ref base A (19/23);  new base T (2/3);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

CCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCGGAATCCTCCGGC  >  NC_002947/3070351‑3070642                                                                                                                                                     |                                                                                                                                                  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                                                                                                                                    <  3:56938/146‑1 (MQ=18)                  aCCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTCGCCCGCCCCCACAGGTTCTTCACCGGTTCTGGAACCAGCGGTGAACCTGTGGgag‑c                                                                                                                                    >  4:56938/1‑146 (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)                                                                                                                                     gTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCg              <  3:276654/148‑1 (MQ=255)                                                                                                                                             aCCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCGGAAtcctc      <  3:356631/148‑1 (MQ=255)                                                                                                                                              ccGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCCACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCGGAATCCTCCg    <  2:300472/149‑1 (MQ=255)                                                                                                                                                ggTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCGGAATCCTCCGGc  <  2:278602/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CCACAAGATGATGCTTGACCATTATCAGCAGACCAAGAACCTGCTGGTGAGCTACGACATCAATCCGCTGGGCTTCTTCTAAACCGCGTCGCGGCCTTCGCGGGCTTGCCCGCTCCCACAGGTTCACCGCTGGTTCCAGAACCGGTGAAGAACCTGTGGGGG‑CGGGCGAGC‑CCGCAAAAGGGCCGGCACATGCATGGCCTACCCGTACCAACGCACCCCGCAAGCTCGTTCCAAAGTAGCATTCGGTCCAGTCCGCCCCCGTGCATTAATGCTTCTACCGGAATCCTCCGGC  >  NC_002947/3070351‑3070642

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: ‑