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	85.7%	55.4 / 3.3	29	intergenic (+496/+260)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base G (3/1);  new base A (12/12);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 6.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.04e-01

GAACTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGT  >  NC_000913/3560118‑3560591                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                        gAACGGGGAGATAAAATCGAGCGTCGCTTCGCTAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTTATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATgc                                                                                                                                                                                                                                   <  1:369220/251‑1 (MQ=255)     tGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGctc                                                                                                                                                                                                                               >  1:13173/1‑251 (MQ=255)              aaaTCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCGACGTTGAGATTGGTGGTGACAATGCGCAAATTGCTGTGCTTGAGCAGTGCGTG‑AGCTACCGCTTCGGGCGAGGTGCCGATATCGATAAACAGGGGCGAGCCATTGGGGATTTGGCCAGCCACTTTGCTGCAGATTGGCTCTTTttcttt                                                                                                                                                                                                                      >  2:49861/1‑250 (MQ=255)                   ggggttgcactctccAATGACCCCCCCATCGCGGCGGCGTAATTCGCCACCGGCGAAAATGATGCGAAAATCTTCTTTTACCATCATCGGGTTAGCAGCGTTGAGAATGGTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGC‑TGTCGCGACCGCTTCCGGCGTGGGGCCGATACCGACAAACAGCTTTGAGCCATTGGGGATTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCt                                                                                                                                                                                                                 <  2:285307/238‑1 (MQ=255)                   gatcGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCt                                                                                                                                                                                                                 <  1:116217/248‑1 (MQ=255)                      cGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTggg                                                                                                                                                                                                              >  1:59621/1‑251 (MQ=255)                       gtcactccGCCAACGATCCTGCCAGCGCGGCTGCGTTATTCGCCACCTGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTATAAACGTTGAGTTTGTTGGTTACAATGCGCAAATTGTTTTGATGGATCATTGCGCT‑CGCTACCGCTTCCGGCTTGGTGCCGATAACTATAAACAGCGTCGGGCCATTGGTTATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGt                                                                                                                                                                                                             <  1:371403/244‑1 (MQ=255)                             tCGCCAATGACCCCGCCAGCGCGGCTGCGTAATTCGCCACCGGCGAGAAGGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCTATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTGCTTCGGTCTGGGTGGCCt                                                                                                                                                                                                        <  1:38985/250‑1 (MQ=255)                                                         gTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCAACAACGTGTGAGCAACGTTGATATTTTTGGTAAGAATGCGCAAATTGCTGTGATGGGGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGGGCAAGTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGaa                                                                                                                                                                           <  1:3924/251‑1 (MQ=255)                                                                                   cGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGGTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATAGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCatg                                                                                                                                                 >  1:343271/1‑251 (MQ=255)                                                                                     aaaaTCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTCACCGAACTGGAAGGCAGCGCCGCACCGCCatgat                                                                                                                                               >  1:63878/1‑251 (MQ=255)                                                                                               tttACCATCAACGTTTTAGCAACGTTGAGATTGTTGGTGACAATGCGAAAATTGCTGTGATGGAGCAGTGCGGG‑CGCTCCCGCTTCCGGCGTGGTGCGGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑cgcag                                                                                                                                       <  1:191237/248‑5 (MQ=255)                                                                                                  cccATCACCGTGTTAGAAAGGTTGAGATTGTGGGTGAAAAGGCGCAAATTGTGGTGATTGGGCAGTGCGTG‑CGCTCCCGCTTCCGGGGTGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAg                                                                                                                                 <  1:163058/250‑1 (MQ=255)                                                                                                              ttAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTTATTGAGCAGTGCGTG‑CGCTACCGCTTCAGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGCCACGGCGTGTTAACCGTACTGGCAGGCCGCGCCGCACCGCCATGATGG‑CGCAGGATAAGGTTTTGCTCCGc                                                                                                                     >  2:244434/1‑251 (MQ=255)                                                                                                                                     gACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGa                                                                                               >  1:2186/1‑250 (MQ=255)                                                                                                                                       cAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGact                                                                                             >  1:60126/1‑248 (MQ=255)                                                                                                                                        aaTGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGCGGTCGCGGCGAAt                                                                                             >  1:262865/1‑249 (MQ=255)                                                                                                                                         aTGCGCACATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCAGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTATTTCTTCGGTCTGGGTGGCCTTGCGATCGGTCCACGGCGTGTTAACCGAACTGATAGGCCGAGCCACACCGCCATGCTGGAG‑CCGGCTCAGGGTTGGATCCGCCCGCACATTGCGGTCCCGGCGAATAGt                                                                                          >  2:177686/1‑251 (MQ=255)                                                                                                                                                    gCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑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)                                                                                                                                                                                                     atCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCg                                                                                                                                                      <  1:6233/133‑1 (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)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                        GAACTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTG‑CGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGT  >  NC_000913/3560118‑3560591

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑