Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,252	C→T	18.1%	intergenic (+101/‑66)	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	1,703,252	0	C	T	18.1%	91.8 / 11.4	44	intergenic (+101/‑66)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (18/18);  new base T (3/5);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 7.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAC  >  NC_002947/1703106‑1703400                                                                                                                                                    |                                                                                                                                                      gATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑tt                                                                                                                                                    <  3:105807/149‑1 (MQ=255) gATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTAAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑tt                                                                                                                                                    <  8:160163/149‑1 (MQ=255)  aTCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTg                                                                                                                                                   >  2:312438/1‑149 (MQ=255)  aTCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTg                                                                                                                                                   <  8:121217/149‑1 (MQ=255)     cgcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAGGCCT‑TTGTAg                                                                                                                                                <  4:299699/149‑1 (MQ=255)     cgcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTa                                                                                                                                                 <  2:17751/148‑1 (MQ=255)      gcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAg                                                                                                                                                >  5:61146/1‑148 (MQ=255)       cgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGa                                                                                                                                              <  3:299003/149‑1 (MQ=255)         aCGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGc                                                                                                                                            <  2:126024/149‑1 (MQ=255)           gTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCgg                                                                                                                                          <  1:312438/149‑1 (MQ=255)              aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAGGCCT‑TTGTAGGAGCGGGtt                                                                                                                                       >  6:28784/1‑149 (MQ=255)              aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCgg                                                                                                                                          <  6:291319/146‑1 (MQ=255)              aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCgg                                                                                                                                          >  5:291319/1‑146 (MQ=255)                 cTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTAc                                                                                                                                    <  6:61146/149‑1 (MQ=255)                 cTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTAc                                                                                                                                    <  6:62961/149‑1 (MQ=255)                  tgatCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCATCAAAGGCC‑TTGTAGGAGCGGGTTTaac                                                                                                                                   >  1:288865/4‑147 (MQ=255)                    ttCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGt                                                                                                                                                  <  4:123648/132‑1 (MQ=255)                      cccGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTACCcgc                                                                                                                                <  5:28784/148‑1 (MQ=255)                      cccGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCcgc                                                                                                                                <  2:229504/148‑1 (MQ=255)                       ccGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCAACAAAGGCC‑GTGTAGGAGCGGGTTTACCcgcg                                                                                                                               >  4:271693/1‑148 (MQ=255)                                 gTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCCGGTTTACCCGCGAAGGGGCCAg                                                                                                                     >  3:135463/1‑148 (MQ=255)                                   ccGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAg                                                                                                                                                >  6:196690/1‑119 (MQ=255)                                   ccGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAg                                                                                                                                                <  5:196690/119‑1 (MQ=255)                                                      gAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCgg                                                                                                                                          <  4:19643/106‑1 (MQ=255)                                                                ccTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCAt                                                                                                 >  1:66470/1‑137 (MQ=255)                                                                ccTTTCGAGGCGGCTTTTTCTTGCCTGAAGATTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTACTACAAAGGCC‑TTGTAGGAGCGGGTTTAACCGCGAAGGGGGCACAACTTAAGaaa                                                                                                          >  1:193699/1‑128 (MQ=25)                                                                            gcTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTTAA‑ACCCCGACGAAAAAGGCC‑GTGTTGGAGCGGGGTTTACCGCGAAAGGGGCAGCCCTGACGAAACACCCCCATGAGGTGTCCCCCGTGGCCCCCGcc                                                                         >  4:133716/1‑149 (MQ=255)                                                                                           aatttttATGTTGTCAGAACCGGCCTCTTGGCGGTTAAA‑CCCGCGCATACACAGGCT‑TTTTAGGTGGGGTTTAACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAg                                                            <  5:181701/143‑1 (MQ=255)                                                                                                          attccgggCCTGTTCG‑GGGTAAACCCCGCTGATACACTGGCT‑TTGTAGCAGGGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGc                                            <  2:288865/142‑1 (MQ=255)                                                                                                                   ccctgcgcgGGAAAC‑CCCGCCCCAACAACCCCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTc                                  <  3:269275/144‑1 (MQ=38)                                                                                                                    tctTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCAccgccagag                                 >  5:273575/1‑145 (MQ=255)                                                                                                                    gcgtCGCGGTTAAC‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCAccgc                                      <  6:273575/141‑1 (MQ=255)                                                                                                                           gggTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAg                          >  2:104765/1‑149 (MQ=255)                                                                                                                            gtaaaa‑CCCGGCCCTACAACGGCC‑TTTTGGTTGGGGTTTTACCGGGGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGc                         <  2:234957/146‑1 (MQ=255)                                                                                                                                   cccGCTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGc                                                                     >  5:95500/1‑99 (MQ=255)                                                                                                                                   cccGCTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGc                                                                     <  6:95500/99‑1 (MQ=255)                                                                                                                                   cccGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                   >  4:47258/1‑149 (MQ=255)                                                                                                                                    ccGCTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                   >  2:324613/1‑148 (MQ=255)                                                                                                                                    ccGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                   >  8:93930/1‑148 (MQ=255)                                                                                                                                          cTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAg            >  2:24829/1‑149 (MQ=255)                                                                                                                                             acaaGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCaa             <  4:32072/144‑1 (MQ=38)                                                                                                                                             acaaGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCaa             >  3:32072/3‑146 (MQ=38)                                                                                                                                              aaaGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg        >  4:212125/1‑149 (MQ=255)                                                                                                                                               aaGGCCTTTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg        >  1:42081/1‑149 (MQ=255)                                                                                                                                                    c‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAc  >  6:236700/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                      GATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTACCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAC  >  NC_002947/1703106‑1703400

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: ‑