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	90.9%	58.9 / ‑2.4	22	intergenic (+589/+167)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base G (11/9);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 4.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGCT  >  NC_000913/3560212‑3560697                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   tttACCATCAACGTTTTAGCAACGTTGAGATTGTTGGTGACAATGCGAAAATTGCTGTGATGGAGCAGTGCGGGCGCTCCCGCTTCCGGCGTGGTGCGGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑cgcag                                                                                                                                                                                                                                                 <  1:191237/248‑5 (MQ=255)    cccATCACCGTGTTAGAAAGGTTGAGATTGTGGGTGAAAAGGCGCAAATTGTGGTGATTGGGCAGTGCGTGCGCTCCCGCTTCCGGGGTGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAg                                                                                                                                                                                                                                           <  1:163058/250‑1 (MQ=255)                ttAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTTATTGAGCAGTGCGTGCGCTACCGCTTCAGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGCCACGGCGTGTTAACCGTACTGGCAGGCCGCGCCGCACCGCCATGATGG‑CGCAGGATAAGGTTTTGCTCCGc                                                                                                                                                                                                                               >  2:244434/1‑251 (MQ=255)                                       gACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGa                                                                                                                                                                                                         >  1:2186/1‑250 (MQ=255)                                         cAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGact                                                                                                                                                                                                       >  1:60126/1‑248 (MQ=255)                                          aaTGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGCGGTCGCGGCGAAt                                                                                                                                                                                                       >  1:262865/1‑249 (MQ=255)                                           aTGCGCACATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCAGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTATTTCTTCGGTCTGGGTGGCCTTGCGATCGGTCCACGGCGTGTTAACCGAACTGATAGGCCGAGCCACACCGCCATGCTGGAG‑CCGGCTCAGGGTTGGATCCGCCCGCACATTGCGGTCCCGGCGAATAGt                                                                                                                                                                                                    >  2:177686/1‑251 (MQ=255)                                                      gCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑cg                                                                                                                                                                                                                                                    >  1:70867/1‑191 (MQ=255)                                                                    gtgcggtcgcTACCGCTTCCGGGGTGGTGCCGATACCGTTAACCAGCTGCGAGCCTTGGGGGTTTTGCGCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTACCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                                                                                                                             <  1:16772/242‑1 (MQ=255)                                                                            gcTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGctc                                                                                                                                                                   >  1:233629/1‑251 (MQ=255)                                                                                                  cGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgc                                                                                                                                             >  1:336268/1‑251 (MQ=255)                                                                                                   gATATCGATAAACAGCGTCGAGCAATTGGGAATTTGCCCCGCCTCTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTGGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                                                                                                                                            <  1:107846/251‑1 (MQ=255)                                                                                                     tatCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGt                                                                                                                                          >  1:281881/1‑251 (MQ=255)                                                                                                                   ggcGAGCCATTGGGGCTTTGCTCCGCCACGTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCATGCTGGAG‑CAGGATCAGGGTTTGCTCCGCCAGATCATTGAGGTCGCGGCTACAAGTCTGCGGGCTGAAGGCGAAATTCTCTACCAGCTATTCGGTAATGAGCTAACCATGCTTTTTAAcctattcgc                                                                                                                             >  2:168200/3‑243 (MQ=255)                                                                                                                           gtgggggTTTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGt                                                                                                                    <  1:2017/248‑1 (MQ=255)                                                                                                                             tGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTtg                                                                                                                  >  1:80325/1‑251 (MQ=255)                                                                                                                                    ttgccccgcccttttGCGGACGATGCGCGTTTTTTCTTGGGTGTGGGGGGCTTTGCGATCGTGCCACGGCGTTTTACCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGt                                                                                                            <  1:314400/238‑1 (MQ=255)                                                                                                                                                          aTGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTGTAAATc                                                                                     <  1:49861/251‑1 (MQ=255)                                                                                                                                                                                  gTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCCACTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTAGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTcgcg                                                             >  2:272002/1‑251 (MQ=255)                                                                                                                                                                                          gCGATCGTGCCACGGCGTGTTAACAGAACTGGAAGGCAGCGCCGCACAGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGACGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACACTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAATTCCCTGGAATTATTTTCGTTTTCGCGCATTGAGc                                                     >  1:152405/1‑251 (MQ=255)                                                                                                                                                                                                             ttAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATc                                   <  1:272002/250‑1 (MQ=255)                                                                                                                                                                                                                           gggCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTATTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCt                    <  1:168200/250‑1 (MQ=255)                                                                                                                                                                                                                                   ccgcACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGCCGCGGCGAATAGACCGCGGGCCAACGGCGCAATGCCCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCCTTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGCGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCAGGc            >  1:21562/1‑251 (MQ=255)                                                                                                                                                                                                                                             atgatgG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGCt  <  1:244434/251‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   TTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTGCT  >  NC_000913/3560212‑3560697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑