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%	58.5 / NA	18	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 (6/12);  total (6/12)

TACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGC  >  NC_000913/3560214‑3560696                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                   tACCATTAACGTGTTAGCAACGTTGAGTTTGTGGGTGACAATGCGCAAATTGCTGGGATGGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCAATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAAt                                                                                                                                                                                                       <  1:248514/288‑1 (MQ=255)                                       cAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGGAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                                                                                                                                                 <  1:296133/288‑1 (MQ=255)                                                                    gcgtgcgCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGCGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGt                                                                                                                                                                                                                                         <  1:125586/187‑1 (MQ=255)                                                                    gcgtgcgCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTACGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                                                                                                                                            <  1:379896/200‑1 (MQ=255)                                                                        gcgcTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGCTCAg                                                                                                                                                                                                                                           >  1:172250/1‑181 (MQ=255)                                                                                                                         aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTGCGGTCTGGGTGGCCTTGCGAGCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTa                                                                                                                                                            <  1:462738/211‑1 (MQ=255)                                                                                                                                             cTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGACTTGCGATCGTGCCCCGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCCGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTAGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCa                                                          <  1:430454/288‑1 (MQ=255)                                                                                                                                                  cGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGACGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCCCTTCGGTACTGACATAACCCTTCTGTTTAACCAGTTCGCGAATACCGGTTTGACGTTGGGTTTTCGTTATTTATAAAACCCTTGGAATttttttttttttttcgtttttt                                                      >  2:519112/1‑278 (MQ=255)                                                                                                                                                                                       ggcgtgcggtccACGGCGTGTCAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCGCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAAc                <  1:519112/278‑1 (MQ=255)                                                                                                                                                                                         cGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTc                                                                                                                                                                                                                <  2:162010/95‑1 (MQ=255)                                                                                                                                                                                         cGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTc                                                                                                                                                                                                                >  1:162010/1‑95 (MQ=255)                                                                                                                                                                                             cGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATTAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTCCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGc           <  1:504199/287‑1 (MQ=255)                                                                                                                                                                                                  gagggggtgcTAACCCAAATGGGACGCAGGCGCCCAACCGCAAGGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGGGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCGTTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGc           <  2:237195/277‑1 (MQ=255)                                                                                                                                                                                                                   aCTGGAAGGCA‑GCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCAC‑TGGAATTATTTTCGTTTTCGCGCGTTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGc  >  1:237195/1‑274 (MQ=255)                                                                                                                                                                                                                                          ccATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGc                                      <  1:201131/216‑1 (MQ=255)                                                                                                                                                                                                                                          ccATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGc                                      >  2:201131/1‑216 (MQ=255)                                                                                                                                                                                                                                             tgatgGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                                                                                                                                 >  2:304132/1‑75 (MQ=255)                                                                                                                                                                                                                                             tgatgGCGCAGGATCAGGTTTTGCTCCGCAAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                                                                                                                                 <  1:304132/75‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                   TACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCA‑GCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCC‑TGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGC  >  NC_000913/3560214‑3560696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑