Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,866,110	T→A	100%	intergenic (‑20/+160)	rpoS ← / ← nlpD	RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,866,110	0	T	A	100.0%	41.4 / NA	15	intergenic (‑20/+160)	rpoS/nlpD	RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (3/12);  total (3/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCC  >  W3110S.gb/2866044‑2866163                                                                   |                                                      aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:1074069/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:1083590/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:1367788/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:1430964/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:1611683/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:28244/71‑1 (MQ=255) aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                   <  1:335066/71‑1 (MQ=255)     cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac                                                >  1:1655097/1‑70 (MQ=255)     cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac                                                >  1:922359/1‑70 (MQ=255)      acGCTGTGTGGCTCCCTGCGATAACATTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta                                              <  1:1062485/71‑1 (MQ=255)      acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta                                              <  1:1037513/71‑1 (MQ=255)      acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta                                              <  1:1726140/71‑1 (MQ=255)                                 ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact                                               <  1:384008/43‑1 (MQ=255)                                                 tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc   <  1:221681/71‑1 (MQ=255)                                                  cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc  >  1:1770183/1‑71 (MQ=255)                                                                   |                                                      AACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCC  >  W3110S.gb/2866044‑2866163

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑