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	2,807,300	C→T	pseudogene (33/882 nt)	ygaY →	ECK2675:JW5428:b2681; predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,807,300	0	C	T	92.7%	191.9 / 4.5	68	pseudogene (33/882 nt)	ygaY	ECK2675:JW5428:b2681; predicted transporter
Reads supporting (aligned to +/- strand): ref base C (0/5); new base T (0/63); total (0/68)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.15e-01

GGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGG > W3110S.gb/2807261‑2807331

ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2452978/62‑1 (MQ=255)
ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:728833/62‑1 (MQ=255)
ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2494528/62‑1 (MQ=255)
ggCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:2246350/62‑1 (MQ=255)
gCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTgg           <  1:1261786/61‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2590453/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:324766/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2921224/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2838158/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:280023/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2799835/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2719636/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2716275/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:399060/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2572359/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2502590/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2454976/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1044421/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:39295/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2436082/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:489771/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:493959/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:538167/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:53914/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:580558/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:64637/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:647193/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:672736/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:690653/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:720069/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:726536/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:845286/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:923740/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:953951/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2385844/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1052364/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:109918/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1204831/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1391083/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1435284/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1525756/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1674216/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1709495/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1767721/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1773613/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1785259/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1796764/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1816745/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1841177/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1946270/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1890243/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2029207/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2037295/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2201201/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2212106/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2304846/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2326940/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2342733/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2328802/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:233050/49‑1 (MQ=255)

                    cagCATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2330889/49‑1 (MQ=255)

                       cATTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2433431/48‑1 (MQ=255)

                        aTTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:775012/47‑1 (MQ=255)

                        aTTAACCGGTTTATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2637910/47‑1 (MQ=255)

                                 tttATTTTCTGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:885220/38‑1 (MQ=25)

                                 tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1389139/38‑1 (MQ=38)

                                 tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:2353789/38‑1 (MQ=38)

                                 tttATTTTCAGTCGTGGCACAAATTCTGGTTCCACTgg  <  1:1837844/38‑1 (MQ=38)

GGCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGG > W3110S.gb/2807261‑2807331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A