Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,680,409	T→C	10.6%	L384L (TTG→CTG)  Q282Q (CAA→CAG)	PP_2349 → PP_2350 ←	CBS domain‑containing protein LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,680,409	0	T	C	10.6%	121.0 / 4.5	47	L384L (TTG→CTG)  Q282Q (CAA→CAG)	PP_2349 PP_2350	CBS domain‑containing protein LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (21/21);  new base C (3/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGAACACGCCGC  >  NC_002947/2680262‑2680557                                                                                                                                                     |                                                                                                                                                     cccTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGtt                                                                                                                                                     >  4:103999/1‑149 (MQ=255)  ccTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTtg                                                                                                                                                    <  7:110603/149‑1 (MQ=255)   cTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTtgt                                                                                                                                                   >  1:200474/1‑149 (MQ=255)      gttgtGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTtgtg                                                                                                                                                  <  3:103999/147‑1 (MQ=255)             gAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGc                                                                                                                                         >  2:324341/1‑149 (MQ=255)               aCAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTg                                                                                                                                       <  3:145467/149‑1 (MQ=255)                    gCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGcc                                                                                                                                  >  2:6138/1‑149 (MQ=255)                                        cTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCa                                                                                                              <  2:200474/149‑1 (MQ=255)                                         ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCTGGATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTAGCTGGCGCCGGCAGCTACCAGCCGgcg                                                                                                                >  1:67807/1‑147 (MQ=255)                                         ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCgg                                                                                                                                >  4:10964/1‑130 (MQ=255)                                         ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCgg                                                                                                                                <  3:10964/130‑1 (MQ=255)                                         ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAg                                                                                                             >  3:124577/1‑149 (MQ=255)                                           gATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAg                                                                                                             <  1:324341/147‑1 (MQ=255)                                                 gACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGc                                                                                                                                         <  4:303185/113‑1 (MQ=255)                                                 gACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGc                                                                                                                                         >  3:303185/1‑113 (MQ=255)                                                   cAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAg                                                                                                   <  7:247455/149‑1 (MQ=255)                                                              gggTCATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTGGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAg                                                                                        <  2:67807/149‑1 (MQ=255)                                                                       cccAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCt                                                                               >  8:310134/1‑149 (MQ=255)                                                                        ccAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAgg                                                                                                  >  2:202087/1‑129 (MQ=255)                                                                        ccAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAgg                                                                                                  <  1:202087/129‑1 (MQ=255)                                                                        ccAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGc                                                                                                 <  2:133238/130‑1 (MQ=255)                                                                        ccAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGc                                                                                                 >  1:133238/1‑130 (MQ=255)                                                                        ccAGACCGACCT‑GATCACCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTg                                                                              >  1:277008/1‑149 (MQ=255)                                                                            accgaccT‑GATCGCCGGCCTCAAGCGTCAGTTGTTAAGCAAGATAGAGGCTTCAGATAACCGGGTACCAGCGTTGTGACCAGTAGCTGGCGCCGGCAGCGACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAg                                                                                        >  1:218530/1‑135 (MQ=255)                                                                            accgaccT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAg                                                                                        <  2:218530/135‑1 (MQ=255)                                                                              cgaccT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGt                                                                        >  3:261571/1‑149 (MQ=255)                                                                              cgaccT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGt                                                                        <  4:124577/149‑1 (MQ=255)                                                                                       tCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTc                                                                                  >  7:99334/1‑131 (MQ=255)                                                                                       tCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTc                                                                                  <  8:99334/131‑1 (MQ=255)                                                                                                 cAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAg                                                       >  1:134727/1‑148 (MQ=255)                                                                                                         aGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCgg                                              <  4:261571/149‑1 (MQ=255)                                                                                                           ttGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGt                                            <  2:277008/149‑1 (MQ=255)                                                                                                             gCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAgg                                                                                       <  5:223539/104‑1 (MQ=255)                                                                                                             gCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAgg                                                                                       >  6:223539/1‑104 (MQ=255)                                                                                                               tCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGt                                        >  4:272852/1‑149 (MQ=255)                                                                                                                 aGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGt                                        <  3:272852/147‑1 (MQ=255)                                                                                                                     aGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTc                                  >  7:162699/1‑149 (MQ=255)                                                                                                                                       gactggTCACAACGCTGGGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCg                       <  2:269096/138‑1 (MQ=255)                                                                                                                                       gactggTCACAACGCTGGGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCg                       >  1:269096/5‑142 (MQ=255)                                                                                                                                        tctggTCACAACGCTGGGACCAGTCGGTGGCGCCGGCATCTAACAGCCGGGGCATGATCGCGAAGGCCTGTTGCATGGCTTCGGTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGt                              <  8:284441/131‑1 (MQ=255)                                                                                                                                        actggTCACAACGCTGGGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGc               >  5:147144/4‑149 (MQ=255)                                                                                                                                        actggTCACAACGCTGGGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAAATCCGGt                              >  7:284441/4‑134 (MQ=255)                                                                                                                                             tCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGaa          <  1:6138/149‑1 (MQ=255)                                                                                                                                              cccAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGaa          >  6:28366/1‑148 (MQ=255)                                                                                                                                                cAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGaa          >  6:83790/1‑146 (MQ=255)                                                                                                                                                cAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGaa          <  5:83790/146‑1 (MQ=255)                                                                                                                                                    gTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCgg                                              <  7:209834/106‑1 (MQ=255)                                                                                                                                                    gTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCgg                                              >  8:209834/1‑106 (MQ=255)                                                                                                                                                     ttGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGAACAcgccgc  >  7:310711/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGAACACGCCGC  >  NC_002947/2680262‑2680557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑