Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,560,455	+G	intergenic (+589/+167)	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	3,560,455	1	.	G	100.0%	80.4 / NA	23	intergenic (+589/+167)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (13/10);  total (13/10)

TACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCG  >  NC_000913/3560214‑3560688                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                          tACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCCCCGCCATGATGGcgccggatcc                                                                                                                                                                                                                                   >  2:1572/1‑242 (MQ=255)       cAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGtttt                                                                                                                                                                                                                             >  1:315809/1‑251 (MQ=255)          cGTGTTAGCAACGTTGCGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTACCCGCACTGGAAGGCATCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCt                                                                                                                                                                                                                          >  2:418040/1‑251 (MQ=255)           gtgtTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGCTATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑ACTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCCTGATGGCGCAGGATCTGGTTTTGCTc                                                                                                                                                                                                                         >  1:51497/1‑251 (MQ=255)                            aTTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCAGCACCGCCATGATGGCGCCGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGt                                                                                                                                                                                                        >  2:218921/1‑251 (MQ=255)                                                    gCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGGATa                                                                                                                                                                                             >  1:96020/1‑238 (MQ=255)                                                           ttGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGAAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgaga                                                                                                                                                                          >  1:274252/1‑250 (MQ=255)                                                             gAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGCCGAGCAATTGGGGATTTGCGCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGGGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt                                                                                                                                                                       <  1:280618/251‑1 (MQ=255)                                                                  gtgcgtgcGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCCTTGGGGATTTGCTACGCCACTTTGCAGGCGCTGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGACAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctct                                                                                                                                                                  >  1:171433/1‑251 (MQ=255)                                                                          gcTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                                                                                                                                   >  1:86924/1‑194 (MQ=255)                                                                                         gtggtgCCGATATCGATAAACAGCGTCGAGCCATTGGGGCTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACAt                                                                                                                                            >  1:102778/1‑250 (MQ=255)                                                                                                                ggTCGGGCCATTGGGGTTTTGCTCCGCCTCTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTGG‑CGATC‑GTGCCACGGCGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                                                                                                                    <  1:116002/250‑1 (MQ=255)                                                                                                                        attgggggatcgtgcacacctcttggCGGGCGTGGCGCTCTTTTCTTTCGGTCGGGGTGG‑CCTTG‑CGATC‑GTGCCATGGCGTGTTACCCTAACTGGAAGGCAGCGCCGCTCCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCg                                                                                                            <  1:186338/226‑1 (MQ=255)                                                                                                                               gattgccccccccACTTGGCGGGCTATTCGCTTTTTTTCTCCGGTCGGGGTG‑‑CCTTGGCG‑TCTGTGCCACGGCTTTTTACCCGAACTGTAAGGCAGCGCCGCCCCGCCATGATGGCGCTGGATCATGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGGCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATGCCGTTGTGAc                                                                                                     <  2:274252/240‑1 (MQ=255)                                                                                                                                 tttGCTCCGCCACTTTGCGGGCGATACGCTCTTTTTCTTCGGTCTGGGCGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCAGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGt                                                                                                   >  1:348719/1‑251 (MQ=255)                                                                                                                                         gccatgtggCGGGGGATGCGCTCTTGTTCTTGGGT‑TGGGTGGGCCTGG‑CGATC‑GTGCCCTGTGGGGTAAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGGTTAACCAGTTCGATAATACCGTTGTGACGTTGtgtttg                                                                                           <  2:393359/243‑1 (MQ=255)                                                                                                                                          ccACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTTACATTGtgtttgt                                                                                          >  2:8652/1‑251 (MQ=255)                                                                                                                                          ccACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGtgtttgt                                                                                          <  1:1572/251‑1 (MQ=255)                                                                                                                                                               ttttttCTTCGGTCGGGGGGG‑CCTTG‑CGAGC‑GTGCCACGGCGTTTTACCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTg                                                                        <  1:418040/247‑1 (MQ=255)                                                                                                                                                                                gTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAACCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTAATTTATAAATCCCTGGAATTATTTTCGTTTTcgcg                                                    >  1:27032/1‑251 (MQ=255)                                                                                                                                                                                                                acccGAACTGGAAGGCCGCGCAGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCt                       <  1:218921/249‑1 (MQ=255)                                                                                                                                                                                                                  ccGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTaa                     <  1:158444/251‑1 (MQ=255)                                                                                                                                                                                                                               ccgggcccccccGCCATGATGGGGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATTCCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAAc        <  2:281866/241‑1 (MQ=255)                                                                                                                                                                                                                                     cgcACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCg  >  2:114946/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                          TACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGG‑CCTTG‑CGATC‑GTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCG  >  NC_000913/3560214‑3560688

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑