Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,284	A→G	20.5%	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	20.5%	75.7 / 13.6	39	intergenic (+133/‑34)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (14/17);  new base G (5/3);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 4.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGCCAG  >  NC_002947/1703138‑1703431                                                                                                                                                   |                                                                                                                                                     gTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAAACCCCTCCAAAAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCac                                                                                                                                                     >  8:125712/1‑147 (MQ=255)    cGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCAc                                                                                                                                                  <  6:140132/148‑1 (MQ=255)        ggCCTGAGGGAGCTGAACGCGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTCAAGCTTTATGTGGTCAGTACCGGCCTCTTCGCGGTTAAACCCGCTCCTACAACGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACg                                                                                                                                             <  2:39338/149‑1 (MQ=37)              agtgagCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑accc                                                                                                                                      >  2:165695/1‑147 (MQ=255)                            gcgccgtttCGTGGGGGTTTTTTCTTCCCTCATGTTTTTTGTTGGCGGTACGGCCCTCTGCGGGGTTAACCCCGCTCCTACAACGGCCTTGTTGGCGGGGGTTTACCCGCGAAGGGGCCAGCACTGa                                                                                                                                               <  4:156743/121‑1 (MQ=255)                            gccgccTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCGGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTTACCGCGAAGGGGCCAGCACAGa                                                                                                                                               >  3:156743/1‑127 (MQ=255)                                    tctaGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGCCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGt                                                                                                                  <  7:125712/144‑1 (MQ=255)                                            gcTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCCCACCTACAAAAGCCGTGTAGGAGCGGGTTTACCCGCGAAGGGGCCACCACTGACGAA‑ACACCCCCAAGAGGTATACCCCCTGCCACCCGcc                                                                                                        >  2:1447/1‑149 (MQ=37)                                                           aatcTTTATGTTGTATTTACCGGCCTCTTCGCGGGAAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGTTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAg                                                                                           <  7:197713/144‑1 (MQ=255)                                                              cTTTATTTTGTCATTACCGGCCTCTTCGGGGGTAAACCCGCTCCTACAAAGGCCTTTTAGGTTGGGGTTTACCCGCGAATGGGCCATCACTGAAGAATACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGgcg                                                                                        <  1:202904/148‑1 (MQ=37)                                                              cTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCCCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCCTGAGGTATCCCCCCTGCCCCCCCCCAAGCCTGACCAAGgcgca                                                                                      >  2:202904/1‑148 (MQ=37)                                                                 tATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGcgccg                                                                                     <  5:111175/147‑1 (MQ=255)                                                                   tgttgtCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTCGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGccgccg                                                                                  <  7:84547/148‑1 (MQ=255)                                                                                          cgGGTAAACCCGCTCCTAAAATGGCCTTGTAGGTGTGGGTTTACCCGCGAAGGGGCCATTACTGACGAA‑ACACCTCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGaaa                                                          <  1:83318/149‑1 (MQ=255)                                                                                            ggTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGc                                                        >  3:211560/1‑149 (MQ=255)                                                                                               aaaCCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTg                                                     <  1:162992/149‑1 (MQ=255)                                                                                                aaCCCGCTCCTACAACGGCCTTGTCGGTGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGc                                                    <  1:1447/149‑1 (MQ=255)                                                                                                aaCCCGCTCCTACAAAGGCCTTTTCGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGc                                                    <  1:165695/149‑1 (MQ=255)                                                                                                   ccGCTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                                                  >  5:14481/1‑148 (MQ=255)                                                                                                   ccGCTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                                                  >  7:170885/1‑148 (MQ=37)                                                                                                   ccGCTCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                                                  >  1:252616/1‑148 (MQ=37)                                                                                                     gCTCCTACAAGGCATTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTCACGAA‑ACACCCCCATGACGTATCCCCCGTGACACCCGCCATGCCAGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATAc                                               >  7:132585/1‑149 (MQ=37)                                                                                                       tCCTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCATTACAAAGCCCCCCCCGCCAACCCAACCCCCGACGCCCAAACCGTCCAATAca                                              >  3:190114/1‑147 (MQ=12)                                                                                                         cTACAAGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAg                                           <  6:14481/149‑1 (MQ=255)                                                                                                            cAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGcc                                        >  1:110710/1‑149 (MQ=255)                                                                                                             aaaGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGc                                                                                                         <  3:76203/83‑1 (MQ=255)                                                                                                             aaaGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGc                                                                                                         >  4:76203/1‑83 (MQ=255)                                                                                                             aaaGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg                                       >  2:153215/1‑149 (MQ=255)                                                                                                               aGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATc                                                                             <  2:130897/109‑1 (MQ=255)                                                                                                               aGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATc                                                                             >  1:130897/1‑109 (MQ=255)                                                                                                                  ccTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCa                                                   <  5:63426/132‑1 (MQ=255)                                                                                                                  ccTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCa                                                   >  6:63426/1‑132 (MQ=255)                                                                                                                     tGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAc                                 <  2:252616/147‑1 (MQ=255)                                                                                                                          gAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGa                                                                                                >  3:229904/1‑79 (MQ=37)                                                                                                                          gAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGa                                                                                                <  4:229904/79‑1 (MQ=37)                                                                                                                           aGCGGGTTTACCCGCGAAGAGGCCGGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGcc                         <  8:170885/149‑1 (MQ=255)                                                                                                                             cGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCaa                       <  4:211560/149‑1 (MQ=255)                                                                                                                                      ccGCGAAGGGGCCAGCACTGCCGAA‑ACCCCCCCATGAGGTATCCCCCGTGCCCCCCGCCATGCCTGACCAAGGCGCCGCCGGCCTCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGCCTGCCCGCCAAGGCCGCGaa              >  3:59849/1‑149 (MQ=255)                                                                                                                                                 ccAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGc     >  6:135693/1‑147 (MQ=255)                                                                                                                                                  cAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACAGCCCGCCAAGGCAGCGAACAGCGTCGCCAg  >  2:16936/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     GTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGACTGCCCGCCAAGGCAGCGAACAGCGTCGCCAG  >  NC_002947/1703138‑1703431

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: ‑