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	94.4%	56.0 / ‑2.6	18	intergenic (+589/+167)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (9/8);  total (10/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.89e-01

GTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCG  >  NC_000913/3560226‑3560688                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                          gtTAGCAACGTTGGGAT‑GTTGGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCTCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTcc                                                                                                                                                                                                                        <  1:22847/250‑1 (MQ=255) gtTAGAAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTCCCGCTTCCGGCGTGTTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCGCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGTCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCg                                                                                                                                                                                                                       <  1:202319/251‑1 (MQ=255)   tAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGGGATTGAGCAGTGCGTGCGCTCCCGCTTCCGGCGTGGTGCCGATATCGATAACCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTGGCGATCGTGCCACTGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCg                                                                                                                                                                                                                       <  1:240434/249‑1 (MQ=255)              agaTTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                                                                                                                          <  1:3582/251‑1 (MQ=255)                                  gcAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATAGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCCTGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                                                                                                                       >  1:206488/1‑251 (MQ=255)                                           tgtgATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTc                                                                                                                                                                                                                <  1:300429/217‑1 (MQ=255)                                                                              gtggtgCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAAATGGAGGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGcc                                                                                                                                                                                                                     >  1:45986/1‑177 (MQ=255)                                                                                     agATATCGAAAAACAGCGTCGAGCCATTGGTGATTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGGGGCCTTGCGATCGTGCCACGGCGTTGTAACAGAACTGGAAGTCACCGCCGCACCGCGATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATATTCTGCGGGCTGACGTAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgc                                                                                                                                    <  1:187322/250‑1 (MQ=255)                                                                                           cGATAAACCGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt                                                                                                                               >  1:80782/1‑250 (MQ=255)                                                                                                                                                 gcTCTTTTTCTTCGGTCTGCGTGGCCTTCCGCTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGACATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATCGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTg                                                                        >  1:113807/1‑251 (MQ=255)                                                                                                                                                                        gCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcg                                                                                                                                                                                                      >  1:28669/1‑102 (MQ=255)                                                                                                                                                                            nncGATCGNNCCCCGGCGTGTTAACCGAACTGGAAGCCAGCGCCCCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcg                                                                                                                                                                                                      <  2:28669/96‑1 (MQ=255)                                                                                                                                                                                  cGTGCCCCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTTCTGGCCGACGGAGAAATGCGCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTGCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATc                                       <  1:293956/251‑1 (MQ=255)                                                                                                                                                                                                  aaCCGAACTGGCAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCt                       >  1:127586/1‑251 (MQ=255)                                                                                                                                                                                                         cTGGAAGGCAGCGCCGCACCGCCATGATGGAG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAAccc                 >  1:280414/1‑250 (MQ=255)                                                                                                                                                                                                                 cAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATATCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAAc        >  1:354439/1‑251 (MQ=255)                                                                                                                                                                                                                      ccgcACCGCCATGATGA‑CGCAGGATCAGGTTTTGCTCCGCAAGCTCATTGAGGACGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTAttttcgttttc                                                       >  1:112767/1‑199 (MQ=255)                                                                                                                                                                                                                       cgcACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGAGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATCCCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCg  >  1:140213/1‑251 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                          GTTAGCAACGTTGAGATTGTTGG‑TGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCG  >  NC_000913/3560226‑3560688

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑