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	95.8%	155.0 / 0.2	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 . (0/2);  new base G (26/20);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 2.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.16e-01

CTGCTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAGCGCC  >  NC_002947/3845558‑3845845                                                                                                                                                     |                                                                                                                                               ctgctgTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAATACGTGTTTC‑GC‑ggg                                                                                                                                             <  1:294120/149‑2 (MQ=255)  tgctgTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GC‑gggc                                                                                                                                            >  5:327888/1‑147 (MQ=255)    ctgTCGGCATGATCACTTGCGGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GC‑gggc                                                                                                                                            <  8:11905/147‑3 (MQ=255)    ctgTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GC‑gggct                                                                                                                                           <  3:346585/148‑4 (MQ=255)      gTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGAt                                                                                                                                         >  7:294301/1‑149 (MQ=255)         ggCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCa                                                                                                                                      >  2:183271/1‑149 (MQ=255)         ggCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCa                                                                                                                                      >  7:217945/1‑149 (MQ=255)         ggCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCa                                                                                                                                      >  5:340344/1‑149 (MQ=255)               aTCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGt                                                                                                                                  >  4:123387/1‑147 (MQ=255)                tCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGtggc                                                                                                                               >  8:10337/1‑146 (MQ=255)                   cTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCa                                                                                                                            >  8:187472/1‑149 (MQ=255)                       ccggCTCTGCAAGCCATCGCGCAGGCCGACTTCTTTGATTGT‑TATTGTTGTCATCGCTGTCTCTCTGTCTGTAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCTGGCTGATCCATCGTCAGCCACGa                                                                                                                         <  4:162412/146‑1 (MQ=255)                       cAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGAt                                                                                                                        <  7:187472/149‑1 (MQ=255)                       cAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGAt                                                                                                                        <  6:180077/149‑1 (MQ=255)                           ctctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGAt                                                                                                                    <  2:26741/149‑1 (MQ=255)                            tctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTGTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGa                                                                                                                     >  1:246133/1‑148 (MQ=255)                            tctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGAt                                                                                                                    >  7:155557/1‑148 (MQ=255)                            tctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCACCCACGATGGag                                                                                                                    >  6:324305/1‑147 (MQ=255)                               gCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGc                                                                                                                >  5:212085/1‑149 (MQ=255)                                cAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTGGCTGACGATGGATCa                                                                                                                  <  3:238630/146‑1 (MQ=255)                                cAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGcc                                                                                                               >  7:193280/1‑149 (MQ=255)                                 aaGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGccc                                                                                                              <  5:129460/149‑1 (MQ=255)                                   gCCATGGCGATGGCCGACTTTATTGATTGT‑TATTGTTGTCATCGCGGTCTGTCTGTGTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGAt                                                                                                                                         <  1:319502/120‑1 (MQ=255)                                                ccGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGcc                                                                                               >  6:346752/1‑149 (MQ=255)                                                       cATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCat                                                                                        >  4:265686/1‑148 (MQ=255)                                                         ttgattgT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGAt                                                                                                                    >  4:311451/1‑119 (MQ=255)                                                         ttgattgT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGAt                                                                                                                    <  3:311451/119‑1 (MQ=255)                                                           gatttT‑TTTTGTTGTCATCGCGGTCTCTCTTTCTGAAGGGTTGCGCCAGACTAAGAGCTGGATGACGGGCATAAAACCCGGGTTTCGGG‑GGCTTATCCATCGTCAGCCACTTTGTATCAGCCCGCGCCCTGCCAGGCCGGTGCACgca                                                                                     <  6:327888/148‑1 (MQ=255)                                                           gattgT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGtgcatgca                                                                                     <  3:265686/148‑1 (MQ=255)                                                               gt‑tattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCaa                                                                                 <  5:346752/148‑1 (MQ=255)                                                                  tattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAg                                                                              >  7:313700/1‑149 (MQ=255)                                                                       ttgcCAGCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATCACGGGCAGAAAAGCCGTGTTGC‑GCGGGCTTATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAggtgg                                                                          <  1:99871/148‑1 (MQ=255)                                                                         gtCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAACGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTc                                                                        <  6:340344/148‑1 (MQ=255)                                                                         gtCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTc                                                                        >  7:91243/1‑148 (MQ=255)                                                                          tCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTc                                                                        >  4:89926/1‑147 (MQ=255)                                                                                 ggactctgtGTCTCACGGTTTGCGCCTCACTAATAGCTGCTTTCGGGGCACAAAACCCGTGTTGCGGG‑GGCTTATCCATCGTCCGCCACTATGCATAAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGgcg                                                               <  8:217945/146‑1 (MQ=255)                                                                                        ctgtttgAAGCTTTGCGCAATACAAAGAGCTGTATCACGGCAAGAAAAGACGTTTTTC‑GCGGGCTTATCCATCGTCTCCAACTATGTATAAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCgccgagc                                                         <  2:292686/148‑1 (MQ=255)                                                                                           tctgAAGCGTTGCGCAAGACTAAGAGCTGCATGACGGCCATAAACCCCGTGTTTC‑CCGGGCTCACCCACCGTCCGCCACTTTGCATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCgccgagcc                                                        <  2:91854/146‑1 (MQ=255)                                                                                             tgAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAg                                                   >  4:20260/1‑149 (MQ=255)                                                                                              gAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGc                                                  >  5:196537/1‑149 (MQ=255)                                                                                                        gcCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCgtgt                                        >  8:337497/1‑149 (MQ=255)                                                                                                                   agCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCgcgc                             <  3:123387/149‑1 (MQ=255)                                                                                                                    gCTGGATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCCCCATGGATCAGCCCGCGCCCTTGCAGGCCCGTGCAAGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCCGGAGCGTGTGCCGGgcgcgc                             >  8:289405/1‑148 (MQ=255)                                                                                                                        gATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGTATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTcgc                               <  6:168159/142‑1 (MQ=255)                                                                                                                        gATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCCCGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCCACAGCGAGCCCGTGTGCCCGTCGCCCATGCa                        >  8:153787/1‑149 (MQ=255)                                                                                                                        gATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTcgc                               >  5:168159/1‑142 (MQ=255)                                                                                                                        gATGACGGGCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCa                        <  1:47411/149‑1 (MQ=255)                                                                                                                              gggCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGAc                  <  7:337497/149‑1 (MQ=255)                                                                                                                               ggCAGAAAAGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACg                 <  1:45945/149‑1 (MQ=255)                                                                                                                                   gAAACGACGTGTTTC‑GCGGGCTGAACCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAAtt             <  7:153787/149‑1 (MQ=255)                                                                                                                                    aaaaGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCgt                                          >  5:102185/1‑119 (MQ=255)                                                                                                                                      aaGACGTGTTTC‑GCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCAc          >  5:196014/1‑149 (MQ=255)                                                                                                                                              tttC‑GCGGGCTGATCCAGCGTCACCCACTTTGCATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAGCGcc  <  8:91243/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                               CTGCTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGT‑TATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTC‑GC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCATGCAGATGACGAATTCACCAAGCGCC  >  NC_002947/3845558‑3845845

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: ‑