Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,866,110	T→A	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%	114.1 / NA	36	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 (24/12);  total (24/12)

CCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAA  >  W3110S.gb/2866062‑2866159                                                 |                                                  cccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGc                                      >  1:4450623/1‑62 (MQ=255) cccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGc                                      >  1:210738/1‑62 (MQ=255) cccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAATCTACTAAGGc                                      >  1:226093/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTGCAATTCTACTAAGGcc                                     >  1:4582069/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc                                     >  1:4500840/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc                                     >  1:2175599/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc                                     >  1:704957/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc                                     >  1:4546995/1‑62 (MQ=255)  ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc                                     >  1:911422/1‑62 (MQ=255)        aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt                                 <  1:275904/60‑1 (MQ=255)             aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           <  1:115945/61‑1 (MQ=255)             aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           <  1:4254313/61‑1 (MQ=255)             aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           <  1:876566/61‑1 (MQ=255)             aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           >  1:3273970/1‑61 (MQ=255)             aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           <  1:153826/61‑1 (MQ=255)                 ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa                           <  1:635056/57‑1 (MQ=255)                        ggCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc               >  1:4573605/1‑62 (MQ=255)                        ggCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc               >  1:2542614/1‑62 (MQ=255)                        ggCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc               >  1:1433400/1‑62 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:133842/1‑50 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:4654066/1‑50 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:49748/1‑50 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:3754834/1‑50 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:2616747/1‑50 (MQ=255)                           cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa                        >  1:1550574/1‑50 (MQ=255)                              aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct         >  1:4399370/1‑62 (MQ=255)                              aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct         >  1:4288617/1‑62 (MQ=255)                              aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct         >  1:3845640/1‑62 (MQ=255)                              aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct         >  1:2568909/1‑62 (MQ=255)                              aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct         >  1:631363/1‑62 (MQ=255)                                    aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa   <  1:916785/62‑1 (MQ=255)                                    aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa   <  1:503618/62‑1 (MQ=255)                                    aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa   <  1:3894908/62‑1 (MQ=255)                                    aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa   <  1:3833134/62‑1 (MQ=255)                                      cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa  <  1:298632/61‑1 (MQ=255)                                      cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa  <  1:1556614/61‑1 (MQ=255)                                                 |                                                  CCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAA  >  W3110S.gb/2866062‑2866159

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: ‑