Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,703,252	C→T	21.5%	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	21.5%	91.7 / 21.8	51	intergenic (+101/‑66)	lysS/PP_1497	lysine‑‑tRNA ligase/TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (22/18);  new base T (6/5);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.46e-01

GATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAC  >  NC_002947/1703106‑1703400                                                                                                                                                   |                                                                                                                                                       gATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑tt                                                                                                                                                     <  2:37672/149‑1 (MQ=255)  aTCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTGCTGGCCCCTTCGCGGGTAAACCCGCTCCTAC‑AAGGCC‑tttg                                                                                                                                                   <  5:298899/149‑3 (MQ=38)  aTCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTAC‑AAGGCC‑tttg                                                                                                                                                   <  2:229205/149‑3 (MQ=255)     cgcgACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTTCTACAAAGGCC‑TTGTAg                                                                                                                                                 <  2:231281/149‑1 (MQ=255)        gACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCTT‑TTGTAGGAg                                                                                                                                              >  4:120242/1‑149 (MQ=255)         aCGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGc                                                                                                                                             <  7:71080/149‑1 (MQ=255)            tCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCTT‑TTGTAGGAGCggg                                                                                                                                          <  3:120242/149‑1 (MQ=255)              aTCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGtt                                                                                                                                        <  1:217925/149‑1 (MQ=255)                 cTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCTCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTa                                                                                                                                      <  8:323693/148‑1 (MQ=255)                    ttCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑ccc                                                                                                                                  <  6:380323/148‑1 (MQ=255)                           acaTGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAggg                                                                                                                          >  4:285298/1‑149 (MQ=255)                               gCGTCCGCAGGCCTGAGTGAGCTGAACGTGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCT‑TTGTAg                                                                                                                                                 >  5:361922/1‑123 (MQ=255)                               gCGTCCGCAGGCCTGAGTGAGCTGAACGTGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCT‑TTGTAg                                                                                                                                                 <  6:361922/123‑1 (MQ=255)                                                  agCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACAcccc                                                                                                    >  7:197843/1‑148 (MQ=255)                                                    cTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCT‑TTGTAGGAGc                                                                                                                                             <  8:207813/106‑1 (MQ=255)                                                    cTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAGGCCT‑TTGTAGGAGc                                                                                                                                             >  7:207813/1‑106 (MQ=255)                                                      gAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTAGAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGa                                                                                                            >  3:102280/1‑136 (MQ=255)                                                       accgcgccgccTTTCGCGGGGGATTTTTCTTGCCTTAAGCTTTATGTTGTCTGTCCCGGCCTCTTCGCGGTAAACCCCGCTCCTACAACGGCC‑TTTTTGGTGGGGTTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGa                                                                                               <  8:197843/143‑1 (MQ=255)                                                       aaCGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCCGCACTGACGAAACACCCCCATGAg                                                                                              >  8:8281/1‑149 (MQ=255)                                                           aGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTAt                                                                                          <  3:285298/149‑1 (MQ=255)                                                                ccTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATccccc                                                                                     >  6:368468/1‑149 (MQ=255)                                                                              tttttCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCAt                                                                       >  4:295860/1‑149 (MQ=255)                                                                                tttCTTGCCTTAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAACGGCC‑TTTTAGGAGGGGTTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATg                                                                      <  7:8281/148‑1 (MQ=38)                                                                                        cggAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑GTGTAGGAGCGGGTTTT‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCCTGAGGTATCCCCCGGGCCACCCGCCCAGCCTGGcc                                                               >  8:217977/3‑147 (MQ=25)                                                                                                            tACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACCCCCCCCTGAGGTATCCCCCGTGACACCCGCCATGCCTGCCCAAGgc                                                          >  3:46255/1‑132 (MQ=255)                                                                                                              ccGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCAccg                                       >  7:271114/1‑149 (MQ=255)                                                                                                                    tctTCGCGGGTAAACCCGCTCCTACAAAGGCC‑GTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACCCCCCCATGAGGTATCCCCCGTGTCCCCCGCCATGCCTGCCCACGGCGCCGCCGGCCTCGCCACCGCCGTCg                                 >  5:201984/1‑149 (MQ=37)                                                                                                                    tctTCGCGGGTAAACCCGCTCCTACAAAGGCC‑GTGTAGGAGCGGGGTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACCCCCCCATGAGGGATCCCCCGTGACACCCGCCATGCCGGCCCAAGGCGCCGCCGGCATCGCCCCCGCCGTCg                                 >  3:296936/1‑149 (MQ=37)                                                                                                                       tctcgGTTAAACCCGCTCCTACAACGCCC‑TTGTAGGAGGGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGc                                <  2:294170/144‑1 (MQ=39)                                                                                                                          cgGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGa                             >  7:118549/1‑147 (MQ=255)                                                                                                                           gggTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGc                                >  1:294170/1‑143 (MQ=255)                                                                                                                           gggTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAg                          >  7:41004/1‑149 (MQ=255)                                                                                                                           cggTAAACCCCCCCCAACAACCGCC‑TTGTCCGCCGGGGTTTACCCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGaaa                           <  5:231269/148‑1 (MQ=255)                                                                                                                               aaaCCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGt                       <  4:154609/148‑1 (MQ=255)                                                                                                                               aaaCCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTg                      >  3:154609/1‑149 (MQ=255)                                                                                                                                aaCCCGCTCCTACAAAGGCC‑TTGTAGGAGCTGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGc                     <  5:368468/149‑1 (MQ=255)                                                                                                                                 ctccGATCCTACAAGGCCT‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGACGGCATCGCCACCGCCGTCGCCGAAAGCGTGc                     <  7:326366/146‑1 (MQ=38)                                                                                                                                  cccGCTCCTACAAAGGCC‑TTGTAGGCGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACCCCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGACAGCGTGCaa                   >  8:268350/1‑149 (MQ=255)                                                                                                                                  cccGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                   >  3:203735/1‑149 (MQ=255)                                                                                                                                   ccGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCaa                   >  7:223175/1‑148 (MQ=255)                                                                                                                                   ccGCTCCTACAAAGGCC‑TTGTAAGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAACGCGTGCaa                   >  7:56186/1‑148 (MQ=255)                                                                                                                                    cGCTCCTACAAGCCAT‑TTCTAGGAGCGGGTTTA‑CCCGCTAAGGGGCCAGCACTGACGAAACACCAACAAGAGCTATCACCAGTCACACCCGCCATGCAACACCAACACGCCGACGGCAACGCCACCGCCGACCCCCAAAGCGTGCaaca                 >  8:326366/1‑147 (MQ=255)                                                                                                                                     gCTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATAc                >  4:319008/1‑149 (MQ=255)                                                                                                                                      cTCCTACAAGGCCT‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGAGGCCGGTACTGACAAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATAc                >  5:247030/1‑148 (MQ=37)                                                                                                                                        acTACAACGGCT‑TTGTCGGTGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCaa             <  6:201984/148‑1 (MQ=255)                                                                                                                                          tACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAgg           >  6:35160/1‑149 (MQ=255)                                                                                                                                             aaaGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg        >  7:254856/1‑149 (MQ=255)                                                                                                                                             aaaGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCg        <  8:41004/149‑1 (MQ=255)                                                                                                                                              aaGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGCCCg        >  8:88424/1‑148 (MQ=255)                                                                                                                                               aGGCCTTTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGc       <  3:319008/149‑1 (MQ=255)                                                                                                                                                ggCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCaa     <  7:217977/149‑1 (MQ=255)                                                                                                                                                  cc‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGCCCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGa   >  6:66594/1‑149 (MQ=255)                                                                                                                                                   c‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAc  >  1:248330/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                       GATCCGCGACGTCATCCTGTTCCCGCACATGCGTCCGCAGGCCTGAGTGAGCTGAACGAGCCGCCTTTCGAGGCGGCTTTTTCTTGCCTGAAGCTTTATGTTGTCAGTACCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGGCC‑TTGTAGGAGCGGGTTTA‑CCCGCGAAGGGGCCAGCACTGACGAAACACCCCCATGAGGTATCCCCCGTGACACCCGCCATGCCTGACCAAGGCGCCGCCGGCATCGCCACCGCCGTCGCCGAAAGCGTGCAATACCAAGGCCGCAAGAC  >  NC_002947/1703106‑1703400

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: ‑