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
A5 F28 I3 R1	375	42.1	2927644	71.4%	2090337	57.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,903,475	C→T	L200L (TTG→TTA)	ygcF ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,903,475	0	C	T	77.4%	227.7 / 66.0	124	L200L (TTG→TTA)	ygcF	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (28/0); new base T (0/96); total (28/96)
Fisher's exact test for biased strand distribution p-value = 2.01e-28
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 124 total aligned reads displayed.

ATTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCCTTTTGGCTAATCGGCTGCAGT  >  W3110S.gb/2903420‑2903514

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1046928/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:2774919/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1717403/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:2113199/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:383642/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:213251/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:262566/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:465481/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1425065/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:47192/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:474246/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:516883/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1379497/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:552302/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:874663/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:853920/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1149380/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:1261444/1‑62 (MQ=255)

atTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACgt                                   >  1:2208315/1‑62 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGTAGt  <  1:1937807/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2465383/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2602810/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2433210/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2667608/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2587065/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2576820/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2483361/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2704780/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1075355/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2737616/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:239623/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2782650/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2814901/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2818824/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2573114/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:400044/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:951375/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:803704/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:754396/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:603846/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:598409/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:55446/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:52344/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:478198/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:421097/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2887726/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:391346/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:390495/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:382825/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:377519/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:367590/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:356639/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2925398/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2916685/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2905860/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1381805/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1681526/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1636899/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:162238/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1611503/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1540046/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1539476/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1456579/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1414036/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1413155/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:138947/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2307193/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1356672/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1329627/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1262924/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1245674/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1212575/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1190781/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1180567/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1128403/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1109830/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1080820/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1735692/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2340849/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2275486/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2273366/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2262058/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2218263/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2205966/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2182933/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2166263/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2139695/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2081578/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2066881/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2020202/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:2004826/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1970029/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1902314/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1877137/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1828408/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1822176/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1819149/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:1715607/61‑1 (MQ=255)

                                  cgcAATGCAGGTATCGATACATAAACGCGTAGCATCTCCCTTCTGGCTAATTGGCTGAAGt  <  1:194339/61‑1 (MQ=255)

                                   gcAATGCAGGTATCGATACATAAACGCGTAGCATCTTCCTTCTGGCTAATTGGCTGAAGt  <  1:983730/60‑1 (MQ=255)

ATTTATGTGTTTGCATCGACAAACGCCAATTACGCGCAATGCAGGTTTCAATGCACAAACGTGTGGCATCATCCTTTTGGCTAATCGGCTGCAGT  >  W3110S.gb/2903420‑2903514

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: `‑`

GATK/CNVnator alignment

N/A