Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,300,163	T→A	11.4%	intergenic (+61/+21)	pvdQ → / ← lpxH	acyl‑homoserine lactone acylase PvdQ/UDP‑2,3‑diacylglucosamine hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,300,163	0	T	A	11.4%	134.2 / 6.8	51	intergenic (+61/+21)	pvdQ/lpxH	acyl‑homoserine lactone acylase PvdQ/UDP‑2,3‑diacylglucosamine hydrolase
Reads supporting (aligned to +/- strand):  ref base T (27/18);  new base A (2/4);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 3.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

ACCGAGGCGCAGATCAAGGCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATCAGCTTGT  >  NC_002947/3300016‑3300305                                                                                                                                                      |                                                                                                                                                aCCGAGGCGCAGATCAAGGCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTg                                                                                                                                                >  1:184376/1‑149 (MQ=255)  ccGAGGCGCAGATCAATGCAGATACTGAGTACCGGGAAGTGGTGATCAGTGAGCTGGACAAGGGGGCGGTAGTCAGCCAACCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGc                                                                                                                                               >  6:342562/1‑149 (MQ=255)        cgcAGATCAAGGCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGCCTC‑GCGGGCAAGCCcgcag                                                                                                                                         <  8:8808/149‑3 (MQ=39)         gcAGATCAAGGCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGAGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAg                                                                                                                                        >  4:308376/1‑149 (MQ=255)                   gCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCTCGCGGGCAAGCCGGCAGGC‑CCCTGTag                                                                                                                              <  4:127866/149‑2 (MQ=38)                   gCAGAGCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAAt                                                                                                                             <  4:95019/149‑1 (MQ=255)                              gTACCGGGAAGTGTTGATCAGTGAGCGTGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCATCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGaaaa                                                                                                                   <  3:76562/148‑1 (MQ=255)                                        gtggtgATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAACCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGgcg                                                                                                        <  5:342562/149‑1 (MQ=255)                                         tggtgATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCAAGTACGCGGGTAAACCCCCACAAAAAGGGGCAT‑CCGGGCTTGCCCGGGAGG‑CCCGGTAATGAAAGTAAAACACGAACGgcc                                                                                                        >  1:282852/1‑148 (MQ=255)                                          ggtgATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGgcgc                                                                                                       <  2:184376/148‑1 (MQ=255)                                           gtgATCAGTGAGCGGGACGAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAAcagggctt                                                                                                     >  1:1100/1‑142 (MQ=255)                                                       cGGGACAAGGGGTCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCt                                                                                         <  8:152240/149‑1 (MQ=255)                                                               gggggCGGTAGTCAGCCAGCCCGGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGCGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCa                                                                                 >  7:53943/1‑149 (MQ=255)                                                                         gTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAgg                                                                       >  3:139150/1‑149 (MQ=255)                                                                           cagccagcCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCGAACTGAAAGCCCTGTTCGTCAACCTGCAAGGc                                                                      <  3:308376/148‑1 (MQ=255)                                                                            agccagccCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGccc                                                                    <  2:282852/149‑1 (MQ=255)                                                                            agccagccCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGccc                                                                    <  8:147849/149‑1 (MQ=255)                                                                             gccagccCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGccc                                                                    >  3:46723/1‑148 (MQ=255)                                                                              ccagccCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCaa                                                                  >  7:157772/1‑149 (MQ=255)                                                                                  cccTGTGGGGTCAGCCTGGGCCGGCCCA‑TTCGGGGGTAACCCCGTTCCAACTGGGGCCG‑GGGGTTTTGCCGGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACgg                                                                                                          <  5:192103/105‑1 (MQ=255)                                                                                  cccTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGTTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACgg                                                                                                          >  6:192103/1‑105 (MQ=255)                                                                                       aGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCgcggc                                                           <  1:109844/147‑1 (MQ=255)                                                                                       aGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCgcggc                                                           >  2:109844/1‑147 (MQ=255)                                                                                       aGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGcggcgg                                                         >  5:114039/1‑149 (MQ=255)                                                                                            tCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCa                                                                                 <  7:223642/120‑1 (MQ=255)                                                                                            tCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCa                                                                                 >  8:223642/1‑120 (MQ=255)                                                                                                ccTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCg                                                >  2:281129/1‑149 (MQ=255)                                                                                                       cGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCa                                         <  8:157772/149‑1 (MQ=255)                                                                                                           ccA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGa                                      >  4:304648/1‑148 (MQ=255)                                                                                                                    gggTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTg                             >  6:128639/1‑149 (MQ=255)                                                                                                                    gggTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTg                             >  6:123233/1‑149 (MQ=255)                                                                                                                    gggTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTg                             <  6:114039/149‑1 (MQ=255)                                                                                                                        aaaCCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCgg                         >  6:139698/1‑149 (MQ=255)                                                                                                                           cccGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTg                      <  1:135821/149‑1 (MQ=255)                                                                                                                            ctgacattACAGGGCCTC‑GCGGGCAAGCCCGCAGGC‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTgg                     >  7:286276/8‑149 (MQ=37)                                                                                                                               acattACAGGGCCTC‑GCGGGCAAGCCCGC‑AGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGTGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCa                  >  6:237013/5‑148 (MQ=38)                                                                                                                                   tACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCa                                         <  1:88363/122‑1 (MQ=255)                                                                                                                                   tACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCa                                         >  2:88363/1‑122 (MQ=255)                                                                                                                                     cAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGAc             >  3:326122/1‑148 (MQ=255)                                                                                                                                      aGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGc                                               >  3:167306/1‑113 (MQ=255)                                                                                                                                      aGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGc                                               <  4:167306/113‑1 (MQ=255)                                                                                                                                      aGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGAcc            >  8:130197/1‑148 (MQ=255)                                                                                                                                        gggCCT‑GCGGGCTTGCCCGCGAGGCCCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCAt          >  5:219056/1‑149 (MQ=255)                                                                                                                                        gggCCT‑GCGGGCTTGCCCGCGAGGCCCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCAt          >  3:342771/1‑149 (MQ=255)                                                                                                                                        gggCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATc         >  7:250830/1‑149 (MQ=255)                                                                                                                                          gCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCaa                                                                                >  6:208927/1‑76 (MQ=255)                                                                                                                                          gCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCaa                                                                                <  5:208927/76‑1 (MQ=255)                                                                                                                                             tcgCGGGCAAGCCCGC‑AGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAg                                                                        <  4:283989/79‑1 (MQ=38)                                                                                                                                             t‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATCAGCtt    >  4:146805/1‑149 (MQ=255)                                                                                                                                               gCGGGCAAGCCCGC‑AGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGTGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATCAGCTtgt  <  5:237013/149‑1 (MQ=255)                                                                                                                                                 gggCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATCAGCTtgt  <  7:130197/148‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                ACCGAGGCGCAGATCAAGGCAGATCCTGAGTACCGGGAAGTGGTGATCAGTGAGCGGGACAAGGGGGCGGTAGTCAGCCAGCCCTGAGGCGTCAGCCTGCGCCGGCCCA‑TTCGCGGGTAAACCCGCTCCTACAGGGGCCT‑GCGGGCTTGCCCGCGAGG‑CCCTGTAATGTCAGGAAAACTCGAACGGCGCCAACTGAAAGCCCTGTTCGTCAACCTGCAAGGCCCAACCGCGGCGGTCCCAGTCGCCCAGCACGATACGCCGTGCCGGCTGGCCATCGACCATCAGCTTGT  >  NC_002947/3300016‑3300305

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: ‑