Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,680,403	C→A	11.1%	P382T (CCA→ACA)  W284C (TGG→TGT)	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	2,680,403	0	C	A	11.1%	133.7 / 7.1	45	P382T (CCA→ACA)  W284C (TGG→TGT)	PP_2349 PP_2350	CBS domain‑containing protein LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (19/21);  new base A (3/2);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 6.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CTGCCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGAA  >  NC_002947/2680259‑2680549                                                                                                                                                  |                                                                                                                                                   ctgcCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGc                                                                                                                                                <  4:130323/149‑1 (MQ=255) ctgcCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGc                                                                                                                                                <  7:40952/149‑1 (MQ=255)    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                                                                                                                        <  3:10964/130‑1 (MQ=255)                                            ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCgg                                                                                                                        >  4:10964/1‑130 (MQ=255)                                            ttGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAg                                                                                                     >  3:124577/1‑149 (MQ=255)                                              gATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAg                                                                                                     <  1:324341/147‑1 (MQ=255)                                                    gACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGc                                                                                                                                 >  3:303185/1‑113 (MQ=255)                                                    gACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGc                                                                                                                                 <  4:303185/113‑1 (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                                                                          <  8:99334/131‑1 (MQ=255)                                                                                          tCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTc                                                                          >  7:99334/1‑131 (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)                                                                                                                                                  |                                                                                                                                                   CTGCCCTTGTTGTGCGAACAAGGCCTGCACTGCTTGCCGGTGCTTGATGGCGACAAGCTGGTGGGGGTGATCACCCAGACCGACCT‑GATCGCCGGCCTCAAGCGTCAGTTGCTCAGCAAGATCGAGGCTTCAGATAACCGGGTCCCAGCGTTGTGACCAGTCGCTGGCGCCGGCAGCTACCAGCCGGCGCAGGATCGCGAAGGCCTGTTGCAGGGCTTCGCTGTCGCGTTTGCGTGGGTACACCAGGAAGGTCGGGTAGGTGAACTCCGGTGCCTGCGGTACCCGCTCGAA  >  NC_002947/2680259‑2680549

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: ‑