Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,250	G→C	18.2%	intergenic (+99/‑68)	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	1,703,250	0	G	C	18.2%	78.2 / 14.5	44	intergenic (+99/‑68)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (16/20);  new base C (5/3);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 4.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.02e-01

TCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCG  >  NC_002947/1703104‑1703394                                                                                                                                                   |                                                                                                                                                  tCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGcc                                                                                                                                                 <  1:39257/149‑1 (MQ=255)  cGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCt                                                                                                                                                >  6:111175/1‑149 (MQ=255)        gcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCACCTACAAAGGCCTTTTAg                                                                                                                                           >  8:197713/1‑148 (MQ=255)         cgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGa                                                                                                                                         <  5:98828/149‑1 (MQ=255)         cgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGa                                                                                                                                         <  2:139217/149‑1 (MQ=255)         cgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGa                                                                                                                                         <  6:94045/149‑1 (MQ=255)          gACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAg                                                                                                                                        <  3:192465/149‑1 (MQ=255)          gACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAg                                                                                                                                        >  2:83318/1‑149 (MQ=255)             gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCgg                                                                                                                                     <  5:84764/149‑1 (MQ=255)             gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCgg                                                                                                                                     <  3:50708/149‑1 (MQ=255)              tCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCggg                                                                                                                                    <  6:151002/149‑1 (MQ=255)                      ttCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCcg                                                                                                                            >  2:162992/1‑149 (MQ=255)                                tGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGcc                                                                                                                  >  1:77665/1‑149 (MQ=255)                                   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)                                                         aaCGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGt                                                                                                                                             >  8:134519/1‑97 (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                                                                    >  4:76203/1‑83 (MQ=255)                                                                                                                                               aaaGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGc                                                                    <  3:76203/83‑1 (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)                                                                                                                                                   |                                                                                                                                                  TCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAA‑ACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCG  >  NC_002947/1703104‑1703394

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: ‑