Sample Resequencing Stats

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
A6 F28 I1 R1	58	121.6	3649812	78.1%	2850503	56.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	1,126,916	T→G	intergenic (‑283/+1)	pheS ← / ← pheM	phenylalanine tRNA synthetase, alpha subunit/phenylalanyl‑tRNA synthetase operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,126,916	0	T	G	76.1%	179.8 / 38.2	67	intergenic (‑283/+1)	pheS/pheM	phenylalanine tRNA synthetase, alpha subunit/phenylalanyl‑tRNA synthetase operon leader peptide
Reads supporting (aligned to +/- strand): ref base T (16/0); new base G (0/51); total (16/51)
Fisher's exact test for biased strand distribution p-value = 8.90e-16
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

GGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCAT > minE/1126873‑1126957

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGAt                                           >  1:2600135/1‑44 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:2924896/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:3456529/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:2172466/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:2166712/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:358802/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:1985379/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:1958522/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:3040405/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:243616/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:2535235/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:270338/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:2799850/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:1494619/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:809170/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:870662/1‑61 (MQ=255)

ggCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTaaa                          >  1:1231647/1‑61 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2992546/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3005764/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2991393/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2940894/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3221827/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3353399/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3406583/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:361186/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3558217/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2686746/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3613104/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:3631006/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:407804/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:423405/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:429257/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:471177/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:518199/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:690475/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:704024/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:717214/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:720491/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:871434/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1997444/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:121770/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1300069/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1344874/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1587408/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1606239/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1705154/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1778461/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1787549/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1821466/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1848532/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1891745/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:1921380/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2928756/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2025171/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2061156/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2142926/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2182988/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2215950/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2370296/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2419094/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2591188/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2638131/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:114083/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2898613/60‑1 (MQ=255)

                         aCGCGCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCCGAAAATAGCAGcat  <  1:3504801/60‑1 (MQ=255)

                          cgcgCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:708838/59‑1 (MQ=255)

                          cgcgCTAGCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:145306/59‑1 (MQ=255)

                                 gCCTCCTGAAGTCAGGTGCTAAAGTAAAAGAAGAAGCGGAAAATAGCAGcat  <  1:2180033/52‑1 (MQ=38)

GGCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAGCCTCCTGGATTCAGGTGCTAAAGTAAAAAAAGAAGCGGAAAATAGCAGCAT > minE/1126873‑1126957

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: `‑`

GATK/CNVnator alignment

N/A