Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,560,443	C→G	intergenic (+577/+179)	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	3,560,443	0	C	G	100.0%	76.0 / NA	26	intergenic (+577/+179)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (6/20);  total (6/20)

TCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTA  >  NC_000913/3560209‑3560680                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                               tcttTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATCGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGcgca                                                                                                                                                                                                                                 <  1:130991/250‑4 (MQ=255)       aCCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCa                                                                                                                                                                                                                           <  1:175713/250‑1 (MQ=255)            cAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGtttt                                                                                                                                                                                                                     <  1:199096/251‑1 (MQ=255)            aacggtgtAAGCAATGTTGAGATTTTTGGTGACACGGCGCAATTTGCTGTGATGGGGCGGTGCG‑TGCGTTCCCGCTTCGGGCGTGG‑GGCCGTGAGCGATAAACTGCGTCGTGCCATTGGTGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTGTTTCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTTTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATTATGGCTCAGGAGCAGGtttt                                                                                                                                                                                                                     <  2:218003/247‑1 (MQ=255)                  gtTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCGATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCtacg                                                                                                                                                                                                               >  1:230495/1‑248 (MQ=255)                       cAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGc                                                                                                                                                                                                          >  1:117030/1‑251 (MQ=255)                        aacgagcagaTTGGTGATGACAAGGCGAAAATGGCGGGGATTGAGCATGGCG‑GGCGATACCTCTTCCGG‑GTGGGTGCAGATAGGGATAATCGGTGTCGAGCCAGTGGGAGTGTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGtttttttccggcagcg                                                                                                                                                                                                         <  2:37355/244‑13 (MQ=255)                              gagaTTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTg                                                                                                                                                                                                    <  1:232558/250‑1 (MQ=255)                                       ggTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                                                                                                                          <  1:111055/251‑1 (MQ=255)                                                    aaaTTGCGGTGATTGAGTAG‑GCGGTGCGCCACCGCTTCCGGCGGTG‑TGCCGATCTCGATAAACAGCTGCGAGCCATTGGGGAGTGGCTCCGCCTCTGTGCGGGCGATGCGCTCTTTTTCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAGCGGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCGCCGCCATCTCAGTGAGGTCGCGGGGAATAGTCTGCgg                                                                                                                                                                             <  2:232172/251‑1 (MQ=255)                                                         gCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                                                                                                                        <  1:101542/251‑1 (MQ=255)                                                         gCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑GGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTGTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTg                                                                                                                                                                         <  1:126332/250‑1 (MQ=255)                                                                  ggggcagggcttgcacgaCCGGTTCAGGCGGGG‑TGCCGATATCGATAAACAGCGTGGAGACATGGGGGATTTGGTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                                                                                                                <  2:261/234‑1 (MQ=255)                                                                  gAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGA‑GGGAGGGCCCCCGCGCCATGATGGGGCAGGGTTCGGGTTTGCTCCGCCCGCCTATTGAGGGCGCGGGGAAGAATCTGGGGGCTGAAGgaagaatg                                                                                                                                                              >  1:46895/1‑245 (MQ=255)                                                                      aGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATAGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTGTTAACCGAACTGGCAGGCAGCGCCGCAGCGCCATGATGGCGCAGGAGCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGCCGGAGAAATGctc                                                                                                                                                           >  2:104460/1‑251 (MQ=255)                                                                                     cGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                                                                                                             <  1:11568/251‑1 (MQ=255)                                                                                          ccGGCGGGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTg                                                                                                                                        <  1:154309/251‑1 (MQ=255)                                                                                                  g‑tgCCGATATCGATAAACCGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGGTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGCAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                                                                                                                >  2:186333/1‑251 (MQ=255)                                                                                                     gCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAccc                                                                                                                               <  1:188755/250‑1 (MQ=255)                                                                                                                        gTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat                                                                                                           >  2:173961/1‑251 (MQ=255)                                                                                                                                       aTTTGCTCCGCCACTTTGCGGGCGATGCGCGCTTTTTGTTCGGGCTGGGGGGCCTTGCGAGCGTGCCACGGCGTGTTAACCGGACTGGAAGGCAGCGCCGCAGCGCGATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACg                                                                                            <  2:166447/251‑1 (MQ=255)                                                                                                                                                           ggCGATGCGCGCTTTTTCTTCGGGCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTTTTTCATTta                                                                          <  2:227135/249‑1 (MQ=255)                                                                                                                                                                   gcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTg                                                                <  2:82996/251‑1 (MQ=255)                                                                                                                                                                                                  aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGaa                                 <  1:225111/251‑1 (MQ=255)                                                                                                                                                                                                    cGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGaagc                               <  2:3973/251‑3 (MQ=255)                                                                                                                                                                                                                                 ggCAGCGCCGCAGCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCTATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTa  <  1:121479/251‑1 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                               TCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCG‑TGCGCTACCGCTTCCGGCGTGG‑TGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTA  >  NC_000913/3560209‑3560680

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: ‑