Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,216	C→T	11.9%	intergenic (+65/‑102)	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	1,703,216	0	C	T	11.9%	98.8 / 5.3	42	intergenic (+65/‑102)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (16/21);  new base T (2/3);  total (18/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.24e-01

GACCGCCTGGTGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACC  >  NC_002947/1703071‑1703362                                                                                                                                                  |                                                                                                                                                   gACCGCCTGGTGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTGAGTACCGGc                                                                                                                                                 >  1:117202/1‑149 (MQ=255)      ccTGGTGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCtt                                                                                                                                            >  5:9451/1‑149 (MQ=255)          gTGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTcgc                                                                                                                                         <  3:168503/148‑1 (MQ=255)           tGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGGCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCgg                                                                                                                                       <  8:175256/149‑1 (MQ=255)           tGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCgg                                                                                                                                       <  4:292667/149‑1 (MQ=255)             aTGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCggg                                                                                                                                      >  1:186858/1‑148 (MQ=255)             aTGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGt                                                                                                                                     >  3:168773/1‑149 (MQ=255)                         aaCTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCt                                                                                                                         <  7:38953/149‑1 (MQ=255)                                  tCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGcc                                                                                                                <  3:167530/149‑1 (MQ=255)                                    gATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCtt                                                                                                              >  6:183816/1‑149 (MQ=255)                                    gATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCtt                                                                                                              <  5:135501/149‑1 (MQ=255)                                     aTCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTGAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTg                                                                                                             <  2:117202/149‑1 (MQ=255)                                      tCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCGCTCCTAC‑AAGGCCtttg                                                                                                            >  3:135716/1‑146 (MQ=38)                                        cgcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAg                                                                                                          <  1:134073/149‑1 (MQ=38)                                        cgcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTa                                                                                                           <  5:183816/148‑1 (MQ=255)                                           gACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAg                                                                                                       <  4:135716/149‑1 (MQ=37)                                            aCGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAGc                                                                                                      <  6:9451/149‑1 (MQ=255)                                              gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAGCgg                                                                                                    <  2:186858/149‑1 (MQ=255)                                              gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCgg                                                                                                    <  3:109098/149‑1 (MQ=255)                                              gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCCTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAGCgg                                                                                                    <  4:35798/149‑1 (MQ=255)                                                 aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGtt                                                                                                 >  1:46314/1‑149 (MQ=255)                                                 aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAAACCCCTCCGACGAAGGGCATGTAGGAGCggggt                                                                                                 >  1:290416/1‑147 (MQ=255)                                                       ttCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCgg                                                                                                    <  3:150419/140‑1 (MQ=255)                                                       ttCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCgg                                                                                                    >  4:150419/1‑140 (MQ=255)                                                                     tCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCgg                                                                                                                                       <  3:233477/91‑1 (MQ=255)                                                                     tCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCgg                                                                                                                                       >  4:233477/1‑91 (MQ=255)                                                                      ccGCTGGCCTGCGTGCCCTCACCCCGCCGCCTTGCGCGGGGGTTTTTGCTTGCCTCAAGATTTATTTGGCCATTCCCGCCCTCTGCGCGGTAAACCCCGCCCCAACAACGCCGTTTTCGGCGGGGGTTAACCCGCGAAGGGGCCAGCAc                                                                            <  2:46314/149‑1 (MQ=255)                                                                      ccGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGt                                                                                                            >  7:66913/1‑117 (MQ=255)                                                                      ccGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGt                                                                                                            <  8:66913/117‑1 (MQ=255)                                                                                        tGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCAt                                                           >  5:101697/1‑148 (MQ=255)                                                                                         gAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCg                                                                                                                              >  4:52320/1‑80 (MQ=37)                                                                                         gAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCg                                                                                                                              <  3:52320/80‑1 (MQ=37)                                                                                               gccgccTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGa                                                                                                        >  6:153607/1‑96 (MQ=255)                                                                                               gccgccTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGa                                                                                                        <  5:153607/96‑1 (MQ=255)                                                                                                              ggcTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCGACAAAGGCCTTGTATGAGCGGGTTTAACCGCGAATGGGGCAGCCCTGACGAAACCCCCCCATGAGGGATCCCCCGTGACCCCCGc                                    >  5:2152/1‑149 (MQ=37)                                                                                                                cTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCCAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGGGCCACCCGCCa                                  >  5:324378/1‑149 (MQ=255)                                                                                                                 tttttCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCa                                                                             >  7:131777/1‑105 (MQ=255)                                                                                                                 tttttCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCCCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAGc                                                                                                      <  7:117343/80‑1 (MQ=18)                                                                                                                 tttttCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCCCTTCGCGGGTAAACCCGCTCCTACAAGGCCTTTGTAGGAGc                                                                                                      >  8:117343/1‑80 (MQ=18)                                                                                                                  ttttCTTGCCTCAAGTTTTTTGTTGGACGTCCCGGCCTATTCGCGGGTAAACCCGCTCCTACAATGGCTTTGTCGGTGGGGTTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCAt                                 <  6:101697/148‑1 (MQ=25)                                                                                                                     tCTTGCCTTATGCTTTATGTTGTCTGTACCGGCCTCTTCGCGTTTAACCCCGCTCCTACAAAGGGCTTGTTGGTGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGcc                              <  6:324378/148‑1 (MQ=37)                                                                                                                          ccTTAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTAAAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGAcc                         <  7:95729/148‑1 (MQ=255)                                                                                                                                                cccGGCCGCTTCCCGGGTAACCCCGCCCCAACAACGGCCTTGTAGGAGCGGGTTAACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCAcc  <  7:31175/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                   GACCGCCTGGTGATGCTGCTGACCAACTCGCCGTCGATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCCTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACC  >  NC_002947/1703071‑1703362

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑