Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	3,845,705	+G	intergenic (‑72/+26)	PP_3394 ← / ← PP_3395	3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,845,703	1	.	G	98.0%	161.6 / ‑3.1	49	intergenic (‑70/+28)	PP_3394/PP_3395	3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (26/22);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

CTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAGC  >  NC_002947/3845561‑3845842                                                                                                                                                |                                                                                                                                              ctgTCGCCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑gggct                                                                                                                                          <  5:19603/148‑4 (MQ=255)    tCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑gggctga                                                                                                                                        <  3:189284/147‑6 (MQ=255)      ggCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCa                                                                                                                                     >  6:353067/1‑149 (MQ=255)         aTGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCg                                                                                                                                  <  3:206125/149‑1 (MQ=255)           gATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGt                                                                                                                                 >  6:162485/1‑148 (MQ=255)            aTCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCa                                                                                                                               <  5:353067/149‑1 (MQ=255)                   gCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCAc                                                                                                                          <  8:353774/147‑1 (MQ=255)                     aGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATg                                                                                                                      >  8:265545/1‑149 (MQ=255)                       gCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCAc                                                                                                                          >  5:332496/1‑143 (MQ=255)                       gCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCAc                                                                                                                          <  6:332496/143‑1 (MQ=255)                         tctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATc                                                                                                                  <  8:192284/149‑1 (MQ=255)                          ctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATgg                                                                                                                     >  5:58191/1‑145 (MQ=255)                          ctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATgg                                                                                                                     <  6:58191/145‑1 (MQ=255)                            gCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGc                                                                                                               >  3:264791/1‑149 (MQ=255)                             cAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCa                                                                                                                 <  8:75022/146‑1 (MQ=255)                             cAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCa                                                                                                                 <  8:130078/146‑1 (MQ=255)                                  cATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCgcgc                                                                                                         >  6:307327/1‑149 (MQ=255)                                   aTCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATgg                                                                                                                     >  3:338876/1‑136 (MQ=255)                                   aTCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATgg                                                                                                                     <  4:338876/136‑1 (MQ=255)                                           ggCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAgg                                                                                                >  3:90260/1‑149 (MQ=255)                                                            gttattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑Gt                                                                                          >  6:187775/1‑137 (MQ=255)                                                            gttattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑Gt                                                                                          <  5:187775/137‑1 (MQ=255)                                                               attgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAgg                                                                          >  3:36668/1‑149 (MQ=255)                                                                   ttgtCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAggtgg                                                                       <  7:265545/148‑1 (MQ=255)                                                                   ttgtCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATAAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAggtgg                                                                       >  2:11797/1‑148 (MQ=255)                                                                        aTCGCGGTCTCTCTGTCTGAAGCGTTTCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATACATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGTCG‑GTG‑CACGCAGCAACa                                                                            >  5:140382/1‑138 (MQ=255)                                                                              ggctctctGTCTCAAGCGTTGCGCCAGACTAAGAGCTGGATGCCGGGCAGAAACGACGTGTTCCGCGGGCTGATCCATCGTCACCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGgcgc                                                           <  5:162485/147‑1 (MQ=255)                                                                               tctctcTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCgcc                                                          >  3:98749/1‑149 (MQ=255)                                                                               tctctcTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCgcc                                                          >  5:6183/1‑149 (MQ=255)                                                                                       tctgAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCgccgagccga                                                   >  3:193733/1‑148 (MQ=255)                                                                                         tgAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACa                                                                            <  5:191012/121‑1 (MQ=255)                                                                                         tgAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACa                                                                            >  6:191012/1‑121 (MQ=255)                                                                                         tgAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAg                                                >  3:339496/1‑149 (MQ=255)                                                                                              cGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTTAAGCAGGCGCCGAGCCGACAGCgaga                                           <  1:11797/149‑1 (MQ=255)                                                                                                      cAGACTAAGGGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGc                                   >  2:120317/1‑149 (MQ=255)                                                                                                      aaGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGc                                   <  4:264791/148‑1 (MQ=255)                                                                                                              gagCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTcgcg                           >  2:236389/1‑149 (MQ=255)                                                                                                               agCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACg                                                                                    >  4:248883/1‑91 (MQ=255)                                                                                                               agCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACg                                                                                    <  3:248883/91‑1 (MQ=255)                                                                                                                 cTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCAt                        <  5:95086/149‑1 (MQ=255)                                                                                                                   ggATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGc                      <  1:236389/149‑1 (MQ=255)                                                                                                                    gATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATg                       <  5:307327/147‑1 (MQ=255)                                                                                                                    gATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATg                       <  4:90260/147‑1 (MQ=255)                                                                                                                         cGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATGGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGa                <  1:120317/149‑1 (MQ=255)                                                                                                                          gggCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGAAAGTCACCGCGCCACTGGTGGTAAAACAGGCGCCGAGCCGACAGCGAGAGAGTGTGGCGGTCGCGCCAGCAGAt                  >  1:122056/1‑148 (MQ=255)                                                                                                                            gCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACg              >  2:282696/1‑148 (MQ=255)                                                                                                                             cAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGaa            >  4:78305/1‑149 (MQ=255)                                                                                                                                  gctcttcgtTTCGG‑GGTTGATCCATGGTCAGCCACTTTGTATAAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCAcc      <  4:178511/142‑1 (MQ=255)                                                                                                                                  aaGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCa        >  7:201907/1‑148 (MQ=255)                                                                                                                                      cGTGTTTCGCGGGCTTATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAg   <  1:282696/149‑1 (MQ=255)                                                                                                                                       gtgtTTCGCGGGCTGATCCATGGTCAGCCACGATGGCTCAGCCCGCGCCCGGCCCGGCCG‑GTG‑CACGCCGCAAAACGTGGTCAAGCAGGCGCCGAGCCGCCAGCGAGCGCGTGTGCCGGTCGCGCATGCAGATGACGCATTCACCAAgc  >  7:216271/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                              CTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCG‑GTG‑CACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAGC  >  NC_002947/3845561‑3845842

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: ‑