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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,967,127	G→T	78.1%	V501V (GTC→GTA)	tktA ←	transketolase 1, thiamin‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,967,127	0	G	T	78.1%	43.6 / 10.9	32	V501V (GTC→GTA)	tktA	transketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand): ref base G (4/3); new base T (8/17); total (12/20)
Fisher's exact test for biased strand distribution p-value = 3.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

CCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTTACGCGCAGAGAAGC  >  minE/1967060‑1967192

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCTTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1168562/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:2129643/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:395459/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:390970/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1302308/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1816989/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:333217/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:3153931/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1813800/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:3121681/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1459535/68‑1 (MQ=255)

ccAGGTTCTGACGGGAGAGGAGCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:1610706/68‑1 (MQ=255)

                   gATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:867034/49‑1 (MQ=255)

                         tGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACg                                          <  1:125759/68‑1 (MQ=255)

                          gCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg                                                                   <  1:2161110/42‑1 (MQ=255)

                             gTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGc                                     <  1:3253154/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTTGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1402776/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:2797177/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:2943917/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:369489/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:2459884/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:3183661/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:2450057/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:100618/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:328527/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1133656/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1355442/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1615258/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:72749/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1464835/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:13890/69‑1 (MQ=255)

                                               tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGGCACACGGACGCCATGTAGACATGTTCggg                   <  1:1980384/69‑1 (MQ=255)

                                                cAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   <  1:1453415/68‑1 (MQ=255)

                                                cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   >  1:51638/1‑68 (MQ=255)

                                                cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   >  1:2326213/1‑68 (MQ=255)

                                                cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   >  1:697245/1‑68 (MQ=255)

                                                cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg                   >  1:3068782/1‑68 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTcac                                             >  1:824840/1‑41 (MQ=37)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:522313/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:3232132/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:2963549/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:287647/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:1898502/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:1956869/1‑69 (MQ=255)

                                                 aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt                 >  1:595338/1‑69 (MQ=255)

                                                    acCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACg                                          <  1:2433625/41‑1 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:3160833/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:269419/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:2287582/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:2272553/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:420151/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:430837/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:2131289/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:2072890/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:678950/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:1757655/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:813678/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:1385953/1‑69 (MQ=255)

                                                                cgctACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTCACGCGCAGAGAAGc  >  1:1131486/1‑69 (MQ=255)

                                                                cgcgACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTTACGCGCAGAGAAGc  <  1:2023194/69‑1 (MQ=255)

                                                                cgcgACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTTACGCGCAGAGAAGc  <  1:1498204/69‑1 (MQ=255)

CCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGTTACGCGCAGAGAAGC  >  minE/1967060‑1967192

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