Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A5 F28 I1 R2	164	48.3	4710601	85.3%	4018142	55.9

BRESEQ :: Evidence

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: `‑`

N/A