Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,284	A→G	11.6%	intergenic (+133/‑34)	lysS → / → PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,703,284	0	A	G	11.6%	103.7 / 5.3	43	intergenic (+133/‑34)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (25/13);  new base G (3/2);  total (28/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.49e-01

CGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGCCA  >  NC_002947/1703141‑1703430                                                                                                                                                 |                                                                                                                                                   cGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTAACCGCGAAGGTGCCAGCACt                                                                                                                                               >  1:261552/1‑149 (MQ=255)  gCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTTAAACCC‑CAACGACAAAGGGCGTGTAGGAGCCGGTTTAACCCCGAAGGGGCCAGccag                                                                                                                                               >  2:229246/1‑145 (MQ=255)             tgagCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAAACCC‑CAACTACAAAAGCCGTGTATGAGCGGGTTTACCCGCGAATGGGCCAGCACTGACGAAACAccc                                                                                                                                   >  4:155832/1‑149 (MQ=38)                 cTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCAt                                                                                                                               >  3:134273/1‑149 (MQ=255)                                    cggcggcTTTTTCTTGCCTTAAGCTTTATGTTGTCAGTACCGCCCTCTTCGCGGGAAACCCCG‑CTCCTACAAAGGCCTTGTAGGAGGGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGacac                                                                                                            <  1:229246/148‑1 (MQ=255)                                              ttCTTGCCTGAAGCTTTATGTTGTCAGTCCCGGCCTCTGCGCGGGTAAACCCG‑CTCCAACAACGGCCTTGTAGGAGCGGGTTAACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGc                                                                                                   <  6:337421/148‑1 (MQ=255)                                                   gCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACCCCCCCATGAGGTATGCCCCGTGGCACCCGCCCTGCCTGAc                                                                                              >  1:109458/1‑148 (MQ=255)                                                       gAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCGACAAAGGCCTTGTAGGAGCGGGGTTTACCGCGAAGGGGCCAGCACGGACGAAACACCCCCCGGAGGTAGGCCCCGGGCCCCCCGCCCTGCCGGGCCAAgg                                                                                         >  8:177327/1‑149 (MQ=25)                                                                tggtgtCCGTCCCGGCGTCTTCGCGGGTAACCCCG‑CTCCTACAACGGCCTTGTCGTCGGGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCATGGCGCCGCCgg                                                                                <  8:196681/146‑1 (MQ=255)                                                                   tgtCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCAt                                                                             >  2:72108/1‑149 (MQ=255)                                                                           ccGGCCCCTTCGCGCG‑AAACCCGCCTCCTCCAACGGCCTTGTCGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCAcc                                                                      <  1:276320/148‑1 (MQ=38)                                                                                 tctTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAg                                                                                          >  7:243711/1‑122 (MQ=255)                                                                                 tctTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAg                                                                                          <  8:243711/122‑1 (MQ=255)                                                                                     cgcgGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCg                                                            >  8:77567/1‑148 (MQ=255)                                                                                       cgGTTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGaaa                                                         <  7:177327/149‑1 (MQ=255)                                                                                            aaaCCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCACGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTg                                                    >  2:69946/1‑149 (MQ=255)                                                                                             aaCCCG‑CTCATACAAAGGCCTTGTAGTCGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGc                                                   <  7:250547/149‑1 (MQ=255)                                                                                                 cG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATa                                               >  8:105895/1‑149 (MQ=255)                                                                                                  g‑CTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATAc                                              >  2:86951/1‑149 (MQ=255)                                                                                                  g‑CTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATAc                                              >  2:148530/1‑149 (MQ=37)                                                                                                  g‑CTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACAAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGgc                                                                                        <  2:55342/107‑1 (MQ=18)                                                                                                  g‑CTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACAAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGgc                                                                                        >  1:55342/1‑107 (MQ=18)                                                                                                  g‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCAt                                                                             <  8:216516/118‑1 (MQ=255)                                                                                                  g‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCAt                                                                             >  7:216516/1‑118 (MQ=255)                                                                                                       cTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCAATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAg                                          >  8:92323/1‑149 (MQ=255)                                                                                                        tACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAgg                                         >  2:305147/1‑149 (MQ=255)                                                                                                           aaaGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg                                      >  2:45807/1‑149 (MQ=255)                                                                                                              ggCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGAGAAACCCGCCATGCCCGGACAACGCGCCGCCGGCATACCCACCGCCGTCGCCGAAAGCCTGCAATACCAAGGCCGCaa                                   >  1:291570/1‑149 (MQ=38)                                                                                                                 cTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGc                                                                                                   <  8:58315/82‑1 (MQ=255)                                                                                                                 cTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGc                                                                                                   >  7:58315/1‑82 (MQ=255)                                                                                                                     tAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGcc                            >  6:70339/1‑149 (MQ=255)                                                                                                                      cggAGGGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGcc                            <  3:155832/147‑1 (MQ=255)                                                                                                                      aGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCACGGCCGCAAGACTGccc                           >  8:181404/1‑149 (MQ=255)                                                                                                                       ggAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGccc                           <  1:72108/148‑1 (MQ=255)                                                                                                                              gTTTACCCGCGAAGAGGCCGGTACTGACAAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAgg                    >  3:144447/1‑148 (MQ=255)                                                                                                                                ttACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCaactcag                 >  4:34006/1‑144 (MQ=255)                                                                                                                                   cccGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCg               >  6:101430/1‑148 (MQ=255)                                                                                                                                    ccGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGaa             >  4:240636/1‑149 (MQ=255)                                                                                                                                    ccGCGAAGAGGCCGGTACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGaa             <  1:148530/149‑1 (MQ=255)                                                                                                                                      gcgAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACa           <  7:105895/149‑1 (MQ=255)                                                                                                                                         aaGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCg        >  4:48328/1‑149 (MQ=255)                                                                                                                                              gCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACAACCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGc    >  1:68529/1‑148 (MQ=255)                                                                                                                                               ccAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGCCa  <  7:77567/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   CGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCG‑CTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGCCA  >  NC_002947/1703141‑1703430

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: ‑