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
A1 F3 I0 R2	260	44.3	3360226	90.5%	3041004	64.6

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,512,687	Δ1 bp	100%	coding (654/1248 nt)	ypdG ←	predicted enzyme IIC component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,512,687	0	G	.	77.8%	30.7 / 13.7	18	coding (654/1248 nt)	ypdG	predicted enzyme IIC component of PTS
Reads supporting (aligned to +/- strand): ref base G (4/0); new base . (2/12); total (6/12)
Fisher's exact test for biased strand distribution p-value = 4.90e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.51e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

CTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAA  >  W3110S.gb/2512633‑2512736

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACgtag                                    >  1:1078561/1‑70 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACgtag                                    >  1:1133417/1‑70 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACgtag                                    >  1:913205/1‑70 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACgtag                                    >  1:8376/1‑70 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:1124109/69‑1 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:955629/69‑1 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:624597/69‑1 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:36507/69‑1 (MQ=255)

ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:1174230/69‑1 (MQ=255)

                aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGTGTGATGACGTAGTACATCGCCAGCATGAc                   >  1:1713590/1‑70 (MQ=255)

                aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc                   >  1:1125386/1‑70 (MQ=255)

                 gCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag                                    <  1:666321/52‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:2497761/66‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:312774/66‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:441390/66‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:505671/66‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:1666377/66‑1 (MQ=255)

                                     ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGaa  <  1:1246695/66‑1 (MQ=255)

CTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAA  >  W3110S.gb/2512633‑2512736

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

N/A