Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,560,362	G→A	intergenic (+496/+260)	rtcR → / ← glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,560,362	0	G	A	100.0%	75.7 / NA	27	intergenic (+496/+260)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/16);  total (11/16)

GAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTT  >  NC_000913/3560125‑3560563                                                                                                                                                                                                                                               |                                                                                                                                                                                                           gagaTAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCttt                                                                                                                                                                                               <  1:95811/251‑1 (MQ=255)      aaaaTCGAGCGTCGCTTCGCCAATGATCCCGACATAGCCACCGCGTAATTCGCCACCGACGAGAATGCTGCAAAAATAATCTTTTAACATCAAAGAGATAGCAACGCTGAGATTGATGG‑TGCCAATGCGCACATTGCTGTGATTGAGCAGTGCGTGCACTACCGCTTCCGGCGTGGTGCCGATCTCGATAAACACCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATgcg                                                                                                                                                                                                     >  1:142769/1‑240 (MQ=255)           cGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCtttt                                                                                                                                                                                              <  1:3469/242‑1 (MQ=255)                                  ccGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCGGTGATTGAGCAGTGCGTGCGCGACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACGTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGt                                                                                                                                                                  <  1:310308/247‑1 (MQ=255)                                             gCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTa                                                                                                                                                    >  1:79575/1‑250 (MQ=255)                                                  gTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTGTTTCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAAcc                                                                                                                                                 <  1:263900/248‑1 (MQ=255)                                                           cACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAgg                                                                                                                                      <  1:127487/250‑1 (MQ=255)                                                             ccGGCGAGAATGATGCGAAAATCTTCTTTTACCATCACCGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGAGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATg                                                                                                                                                                                                       >  1:304048/1‑183 (MQ=255)                                                                                                      gtTAGCAACGTTGGGAT‑GTTGGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCTCACCGCCATGATGGCGCAGGATCAGGTTTTGCTcc                                                                                           <  1:22847/250‑1 (MQ=255)                                                                                                      gtTAGAAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTCCCGCTTCCGGCGTGTTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCGCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGTCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCg                                                                                          <  1:202319/251‑1 (MQ=255)                                                                                                        tAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGGGATTGAGCAGTGCGTGCGCTCCCGCTTCCGGCGTGGTGCCGATATCGATAACCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTGGCGATCGTGCCACTGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCg                                                                                          <  1:240434/249‑1 (MQ=255)                                                                                                        naGCAACGTTGAGATTGTTGG‑AGACAATGCGCAAATTAATGAGATTGAGCAGTGAGTGCGCTAACGCTTCCGGCGCGGTGCCGCTATCGATAAACAGAGTCGAGCACTTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTg                                                                                                                                                                               >  1:70164/2‑164 (MQ=255)                                                                                                                   agaTTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                             <  1:3582/251‑1 (MQ=255)                                                                                                                    gaTTGTTGG‑TGACAATGCGCAAATTGCGGTGATTGGGCAGTGCGTGCGCTACCGCTTCCGGCGTTGTGCCGATATCGGTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGTTGGTCTTGCGAGCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAc                                                                                                                           <  1:60275/204‑1 (MQ=255)                                                                                                                                    tGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGCTTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACgg                                                                                                                                                           >  1:51957/1‑157 (MQ=255)                                                                                                                                       gcAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATAGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCCTGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                          >  1:206488/1‑251 (MQ=255)                                                                                                                                              gCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTttcttc                                                                                                                                                                                         >  1:280125/1‑117 (MQ=255)                                                                                                                                                tgtgATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTc                                                                                   <  1:300429/217‑1 (MQ=255)                                                                                                                                                         gCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGcc                                                                                                                                                                            <  1:51175/119‑1 (MQ=255)                                                                                                                                                          cagggcgtgcnCTANNGCTTNCNGNGTGGTGCCGATATCGATAAACAGCGTCGANCCATTGGGGATTTGCTCCGCCACNNTGNNNACNNTgcgc                                                                                                                                                                                                    <  2:257078/90‑1 (MQ=255)                                                                                                                                                          cAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATgcgc                                                                                                                                                                                                    >  1:257078/1‑94 (MQ=255)                                                                                                                                                                         cGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATg                                                                                                                                                                                                       <  1:96995/76‑1 (MQ=255)                                                                                                                                                                                   gtggtgCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAAATGGAGGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGcc                                                                                        >  1:45986/1‑177 (MQ=255)                                                                                                                                                                                     ggtgCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAccac                                                                                                                        >  1:147226/1‑141 (MQ=255)                                                                                                                                                                                          agATATCGAAAAACAGCGTCGAGCCATTGGTGATTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGGGGCCTTGCGATCGTGCCACGGCGTTGTAACAGAACTGGAAGTCACCGCCGCACCGCGATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATATTCTGCGGGCTGACGTAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgc       <  1:187322/250‑1 (MQ=255)                                                                                                                                                                                                cGATAAACCGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt  >  1:80782/1‑250 (MQ=255)                                                                                                                                                                                                             cGAGCNATTGGNGNNTTGCTCCGCCCCTTTGCGGNCGATGCGCTCTTTTTNTTCGNTCTGGNTGNc                                                                                                                                                                             >  2:141723/1‑66 (MQ=255)                                                                                                                                                                                                                               cTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAgc                                                                                                                                  <  1:99980/91‑1 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                           GAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTT  >  NC_000913/3560125‑3560563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑