Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,903,061	A→T	intergenic (‑38/‑121)	mgrB ← / → yobH	PhoP/PhoQ regulator MgrB/YobH family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,903,061	0	A	T	100.0%	74.9 / NA	20	intergenic (‑38/‑121)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (9/11);  total (9/11)

GCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC  >  NZ_CP009273/1902976‑1903142                                                                                      |                                                                                  gcaagcCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCAt                                                                               <  1:14369/90‑1 (MQ=255) gcaagcCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCAt                                                                               <  1:580165/90‑1 (MQ=255) gcaagcCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCAt                                                                               <  2:174828/90‑1 (MQ=255)      ccAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgtt                                                                          <  1:456613/90‑1 (MQ=255)      ccAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgtt                                                                          <  1:492487/90‑1 (MQ=255)              acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc                                                                  <  2:601400/90‑1 (MQ=255)              acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc                                                                  >  2:358106/1‑90 (MQ=255)              acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc                                                                  >  2:340305/1‑90 (MQ=255)                 aCAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgc                                                               <  1:340305/90‑1 (MQ=255)                          aCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTa                                                      <  1:22394/90‑1 (MQ=255)                             aCCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGt                                                   >  2:253179/1‑90 (MQ=255)                                  tCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGata                                              >  2:7698/1‑90 (MQ=255)                                         tttttCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGc                                       <  1:449896/90‑1 (MQ=255)                                                          cGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCg                      >  2:230511/1‑90 (MQ=255)                                                              tCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCgcttg                  >  2:429990/1‑90 (MQ=255)                                                                  ctacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc              <  2:326932/90‑1 (MQ=255)                                                                   tacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCa             >  2:165123/1‑90 (MQ=255)                                                                   tacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCa             >  1:334212/1‑90 (MQ=255)                                                                              aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc  >  2:233067/1‑90 (MQ=255)                                                                              aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc  <  1:230511/90‑1 (MQ=255)                                                                                      |                                                                                  GCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC  >  NZ_CP009273/1902976‑1903142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑