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.svn
00-basic.txt-prep.sample
00-basic.txt.sample
01-initial.txt.sample
02-initialcmp.txt.sample
Ba10k.sim.sfa
Ba10k.sim1.fq
Ba10k.sim2.fq
Banthracis.10k.fa
Ec10k.sim.sfa
Ec10k.sim1.fq
Ec10k.sim2.fq
Ecoli.10k.fa
README
arbrcrd.36.sfa
arbrcrd.ref.fa
multi-single-line-fasta.awk
simulate-reads.pl

README

## Ba10k.sim.sfa
###############################################################################

$ ~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 10000 -1 36 -2 36 B.anthracis.10k.fa Ba10k.sim1.fq Ba10k.sim2.fq
[wgsim_core] 1 sequences, total length: 10000
gi|30260195|ref|NC_003997.3|	524	G	A	-
gi|30260195|ref|NC_003997.3|	921	A	T	-
gi|30260195|ref|NC_003997.3|	1177	A	C	-
gi|30260195|ref|NC_003997.3|	1836	T	A	-
gi|30260195|ref|NC_003997.3|	4238	T	C	-
gi|30260195|ref|NC_003997.3|	6033	A	C	-
gi|30260195|ref|NC_003997.3|	7173	T	G	-
gi|30260195|ref|NC_003997.3|	7852	A	G	-
gi|30260195|ref|NC_003997.3|	8635	T	A	-
gi|30260195|ref|NC_003997.3|	8687	A	G	-

$ ../src/preprocessor.pl Ba10k.sim1.fq | cut -f 12- -d'_' > Ba10k.sim1.sfa
processed 10000 reads

$ ../src/preprocessor.pl Ba10k.sim2.fq | cut -f 12- -d'_' > Ba10k.sim2.sfa
processed 10000 reads

$ cat Ba10k.sim[12].sfa > Ba10k.sim.sfa


## Ba100k.sim.sfa
###############################################################################

$ ~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 100000 -1 36 -2 36 B.anthracis.100k.fa Ba100k.sim1.fq Ba100k.sim2.fq
[wgsim_core] 1 sequences, total length: 100000
gi|30260195|ref|NC_003997.3|	207	T	G	-
gi|30260195|ref|NC_003997.3|	845	C	A	-
gi|30260195|ref|NC_003997.3|	1712	A	G	-
gi|30260195|ref|NC_003997.3|	2945	A	C	-
gi|30260195|ref|NC_003997.3|	4630	T	G	-
gi|30260195|ref|NC_003997.3|	5589	C	G	-
gi|30260195|ref|NC_003997.3|	6978	A	G	-
gi|30260195|ref|NC_003997.3|	7526	A	-	-
gi|30260195|ref|NC_003997.3|	8583	T	G	-
gi|30260195|ref|NC_003997.3|	8780	A	T	-
gi|30260195|ref|NC_003997.3|	9355	C	G	-
gi|30260195|ref|NC_003997.3|	9482	C	T	-
gi|30260195|ref|NC_003997.3|	11282	T	G	-
gi|30260195|ref|NC_003997.3|	11825	A	C	-
gi|30260195|ref|NC_003997.3|	12297	T	A	-
gi|30260195|ref|NC_003997.3|	16491	G	C	-
gi|30260195|ref|NC_003997.3|	16931	A	G	-
gi|30260195|ref|NC_003997.3|	17732	T	G	-
gi|30260195|ref|NC_003997.3|	18071	G	T	-
gi|30260195|ref|NC_003997.3|	19774	G	C	-
gi|30260195|ref|NC_003997.3|	23745	A	T	-
gi|30260195|ref|NC_003997.3|	23759	T	G	-
gi|30260195|ref|NC_003997.3|	29013	C	G	-
gi|30260195|ref|NC_003997.3|	31139	T	A	-
gi|30260195|ref|NC_003997.3|	31459	G	A	-
gi|30260195|ref|NC_003997.3|	37702	C	T	-
gi|30260195|ref|NC_003997.3|	37747	A	G	-
gi|30260195|ref|NC_003997.3|	39414	T	C	-
gi|30260195|ref|NC_003997.3|	40123	A	G	-
gi|30260195|ref|NC_003997.3|	41126	G	T	-
gi|30260195|ref|NC_003997.3|	41678	T	A	-
gi|30260195|ref|NC_003997.3|	44397	G	T	-
gi|30260195|ref|NC_003997.3|	45537	G	T	-
gi|30260195|ref|NC_003997.3|	45540	G	A	-
gi|30260195|ref|NC_003997.3|	47662	A	T	-
gi|30260195|ref|NC_003997.3|	48119	G	A	-
gi|30260195|ref|NC_003997.3|	48186	A	G	-
gi|30260195|ref|NC_003997.3|	49438	A	T	-
gi|30260195|ref|NC_003997.3|	51652	G	A	-
gi|30260195|ref|NC_003997.3|	51831	C	G	-
gi|30260195|ref|NC_003997.3|	55237	G	C	-
gi|30260195|ref|NC_003997.3|	56705	G	C	-
gi|30260195|ref|NC_003997.3|	58187	A	C	-
gi|30260195|ref|NC_003997.3|	59837	T	A	-
gi|30260195|ref|NC_003997.3|	60682	G	T	-
gi|30260195|ref|NC_003997.3|	61222	G	C	-
gi|30260195|ref|NC_003997.3|	62424	T	A	-
gi|30260195|ref|NC_003997.3|	64257	G	T	-
gi|30260195|ref|NC_003997.3|	64307	G	T	-
gi|30260195|ref|NC_003997.3|	65515	T	C	-
gi|30260195|ref|NC_003997.3|	66960	A	C	-
gi|30260195|ref|NC_003997.3|	67783	A	C	-
gi|30260195|ref|NC_003997.3|	68212	A	C	-
gi|30260195|ref|NC_003997.3|	71360	G	C	-
gi|30260195|ref|NC_003997.3|	72933	C	G	-
gi|30260195|ref|NC_003997.3|	72969	C	A	-
gi|30260195|ref|NC_003997.3|	73059	A	C	-
gi|30260195|ref|NC_003997.3|	74130	A	G	-
gi|30260195|ref|NC_003997.3|	74166	A	C	-
gi|30260195|ref|NC_003997.3|	74811	G	T	-
gi|30260195|ref|NC_003997.3|	76812	A	T	-
gi|30260195|ref|NC_003997.3|	77188	T	C	-
gi|30260195|ref|NC_003997.3|	77938	A	T	-
gi|30260195|ref|NC_003997.3|	77958	G	A	-
gi|30260195|ref|NC_003997.3|	78561	T	G	-
gi|30260195|ref|NC_003997.3|	79383	A	C	-
gi|30260195|ref|NC_003997.3|	80274	T	G	-
gi|30260195|ref|NC_003997.3|	81393	T	G	-
gi|30260195|ref|NC_003997.3|	83547	C	-	-
gi|30260195|ref|NC_003997.3|	83679	T	A	-
gi|30260195|ref|NC_003997.3|	86197	G	A	-
gi|30260195|ref|NC_003997.3|	86465	G	C	-
gi|30260195|ref|NC_003997.3|	87947	A	G	-
gi|30260195|ref|NC_003997.3|	88340	T	A	-
gi|30260195|ref|NC_003997.3|	89705	T	A	-
gi|30260195|ref|NC_003997.3|	89962	T	A	-
gi|30260195|ref|NC_003997.3|	90084	A	G	-
gi|30260195|ref|NC_003997.3|	92769	A	T	-
gi|30260195|ref|NC_003997.3|	93959	A	G	-
gi|30260195|ref|NC_003997.3|	96610	-	G	-
gi|30260195|ref|NC_003997.3|	97707	C	A	-

$ ../src/preprocessor.pl Ba100k.sim1.fq | cut -f 12- -d'_' > Ba100k.sim1.sfa
processed 100000 reads

$ ../src/preprocessor.pl Ba100k.sim2.fq | cut -f 12- -d'_' > Ba100k.sim2.sfa
processed 100000 reads

$ cat Ba100k.sim[12].sfa > Ba100k.sim.sfa


## Ec10k.sim.sfa
###############################################################################

~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 10000 -1 36 -2 36 Ecoli.10k.fa Ec10k.sim1.fq Ec10k.sim2.fq

[wgsim_core] 1 sequences, total length: 10000
gi|49175990|ref|NC_000913.2|	259	G	C	-
gi|49175990|ref|NC_000913.2|	1781	-	G	-
gi|49175990|ref|NC_000913.2|	1843	G	T	-
gi|49175990|ref|NC_000913.2|	1927	C	A	-
gi|49175990|ref|NC_000913.2|	3641	G	A	-
gi|49175990|ref|NC_000913.2|	5139	T	A	-
gi|49175990|ref|NC_000913.2|	5299	G	A	-
gi|49175990|ref|NC_000913.2|	5760	T	G	-
gi|49175990|ref|NC_000913.2|	5764	A	T	-
gi|49175990|ref|NC_000913.2|	6310	C	G	-
gi|49175990|ref|NC_000913.2|	9405	T	G	-


../src/preprocessor.pl Ec10k.sim1.fq | cut -f 12- -d'_' > Ec10k.sim1.sfa
../src/preprocessor.pl Ec10k.sim2.fq | cut -f 12- -d'_' > Ec10k.sim2.sfa
cat Ec10k.sim[12].sfa > Ec10k.sim.sfa


## Ec100k.sim.sfa
###############################################################################

~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 100000 -1 36 -2 36 Ecoli.100k.fa Ec100k.sim1.fq Ec100k.sim2.fq

gi|49175990|ref|NC_000913.2|	563	C	G	-
gi|49175990|ref|NC_000913.2|	1321	G	T	-
gi|49175990|ref|NC_000913.2|	4325	-	C	-
gi|49175990|ref|NC_000913.2|	5026	A	C	-
gi|49175990|ref|NC_000913.2|	9092	C	T	-
gi|49175990|ref|NC_000913.2|	9991	C	A	-
gi|49175990|ref|NC_000913.2|	10382	A	T	-
gi|49175990|ref|NC_000913.2|	11468	T	G	-
gi|49175990|ref|NC_000913.2|	11643	A	G	-
gi|49175990|ref|NC_000913.2|	11815	G	C	-
gi|49175990|ref|NC_000913.2|	11822	A	T	-
gi|49175990|ref|NC_000913.2|	16616	-	CC	-
gi|49175990|ref|NC_000913.2|	18059	A	G	-
gi|49175990|ref|NC_000913.2|	18233	A	G	-
gi|49175990|ref|NC_000913.2|	18345	C	G	-
gi|49175990|ref|NC_000913.2|	19198	C	T	-
gi|49175990|ref|NC_000913.2|	20360	G	C	-
gi|49175990|ref|NC_000913.2|	21029	G	C	-
gi|49175990|ref|NC_000913.2|	22156	C	-	-
gi|49175990|ref|NC_000913.2|	22157	G	-	-
gi|49175990|ref|NC_000913.2|	22158	G	-	-
gi|49175990|ref|NC_000913.2|	22838	T	G	-
gi|49175990|ref|NC_000913.2|	23431	G	C	-
gi|49175990|ref|NC_000913.2|	23501	C	A	-
gi|49175990|ref|NC_000913.2|	24884	G	T	-
gi|49175990|ref|NC_000913.2|	25193	C	T	-
gi|49175990|ref|NC_000913.2|	27669	T	A	-
gi|49175990|ref|NC_000913.2|	28418	G	A	-
gi|49175990|ref|NC_000913.2|	32585	G	A	-
gi|49175990|ref|NC_000913.2|	32629	A	T	-
gi|49175990|ref|NC_000913.2|	34567	C	A	-
gi|49175990|ref|NC_000913.2|	34908	T	C	-
gi|49175990|ref|NC_000913.2|	35028	A	T	-
gi|49175990|ref|NC_000913.2|	35565	-	AA	-
gi|49175990|ref|NC_000913.2|	35852	T	G	-
gi|49175990|ref|NC_000913.2|	36629	C	G	-
gi|49175990|ref|NC_000913.2|	37565	G	C	-
gi|49175990|ref|NC_000913.2|	37771	G	A	-
gi|49175990|ref|NC_000913.2|	38605	A	G	-
gi|49175990|ref|NC_000913.2|	38753	A	G	-
gi|49175990|ref|NC_000913.2|	39565	A	T	-
gi|49175990|ref|NC_000913.2|	40533	C	G	-
gi|49175990|ref|NC_000913.2|	40544	A	T	-
gi|49175990|ref|NC_000913.2|	42148	A	G	-
gi|49175990|ref|NC_000913.2|	42216	A	C	-
gi|49175990|ref|NC_000913.2|	45913	T	G	-
gi|49175990|ref|NC_000913.2|	46520	T	G	-
gi|49175990|ref|NC_000913.2|	47154	C	G	-
gi|49175990|ref|NC_000913.2|	47163	G	A	-
gi|49175990|ref|NC_000913.2|	48605	T	C	-
gi|49175990|ref|NC_000913.2|	50032	T	A	-
gi|49175990|ref|NC_000913.2|	51009	C	G	-
gi|49175990|ref|NC_000913.2|	53921	G	T	-
gi|49175990|ref|NC_000913.2|	55143	T	A	-
gi|49175990|ref|NC_000913.2|	56449	C	T	-
gi|49175990|ref|NC_000913.2|	59805	T	C	-
gi|49175990|ref|NC_000913.2|	60027	G	T	-
gi|49175990|ref|NC_000913.2|	60296	C	A	-
gi|49175990|ref|NC_000913.2|	60598	T	G	-
gi|49175990|ref|NC_000913.2|	60719	C	G	-
gi|49175990|ref|NC_000913.2|	61117	G	C	-
gi|49175990|ref|NC_000913.2|	62094	T	C	-
gi|49175990|ref|NC_000913.2|	62251	A	T	-
gi|49175990|ref|NC_000913.2|	63231	C	A	-
gi|49175990|ref|NC_000913.2|	64373	C	A	-
gi|49175990|ref|NC_000913.2|	65317	A	C	-
gi|49175990|ref|NC_000913.2|	65630	G	T	-
gi|49175990|ref|NC_000913.2|	66608	T	C	-
gi|49175990|ref|NC_000913.2|	66873	G	C	-
gi|49175990|ref|NC_000913.2|	67395	-	T	-
gi|49175990|ref|NC_000913.2|	67907	T	C	-
gi|49175990|ref|NC_000913.2|	68332	C	A	-
gi|49175990|ref|NC_000913.2|	68523	G	A	-
gi|49175990|ref|NC_000913.2|	69046	G	A	-
gi|49175990|ref|NC_000913.2|	70470	C	G	-
gi|49175990|ref|NC_000913.2|	72307	G	C	-
gi|49175990|ref|NC_000913.2|	72599	A	T	-
gi|49175990|ref|NC_000913.2|	72681	A	G	-
gi|49175990|ref|NC_000913.2|	72886	C	T	-
gi|49175990|ref|NC_000913.2|	73149	A	C	-
gi|49175990|ref|NC_000913.2|	73618	A	T	-
gi|49175990|ref|NC_000913.2|	73658	G	T	-
gi|49175990|ref|NC_000913.2|	73762	A	T	-
gi|49175990|ref|NC_000913.2|	74026	G	C	-
gi|49175990|ref|NC_000913.2|	74330	A	G	-
gi|49175990|ref|NC_000913.2|	75149	C	A	-
gi|49175990|ref|NC_000913.2|	75313	C	T	-
gi|49175990|ref|NC_000913.2|	79027	G	C	-
gi|49175990|ref|NC_000913.2|	79788	C	A	-
gi|49175990|ref|NC_000913.2|	80378	C	T	-
gi|49175990|ref|NC_000913.2|	81463	C	G	-
gi|49175990|ref|NC_000913.2|	81638	G	T	-
gi|49175990|ref|NC_000913.2|	83617	C	G	-
gi|49175990|ref|NC_000913.2|	83999	T	G	-
gi|49175990|ref|NC_000913.2|	84698	G	A	-
gi|49175990|ref|NC_000913.2|	86095	C	T	-
gi|49175990|ref|NC_000913.2|	86314	A	T	-
gi|49175990|ref|NC_000913.2|	86846	A	G	-
gi|49175990|ref|NC_000913.2|	87238	A	G	-
gi|49175990|ref|NC_000913.2|	89861	A	C	-
gi|49175990|ref|NC_000913.2|	92217	A	C	-
gi|49175990|ref|NC_000913.2|	92290	C	T	-
gi|49175990|ref|NC_000913.2|	97213	G	T	-
gi|49175990|ref|NC_000913.2|	98048	C	G	-
gi|49175990|ref|NC_000913.2|	98391	G	T	-


../src/preprocessor.pl Ec100k.sim1.fq | cut -f 12- -d'_' > Ec100k.sim1.sfa
../src/preprocessor.pl Ec100k.sim2.fq | cut -f 12- -d'_' > Ec100k.sim2.sfa
cat Ec100k.sim[12].sfa > Ec100k.sim.sfa




## Ec200k.sim.sfa
###############################################################################

~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 200000 -1 36 -2 36 Ecoli.200k.fa Ec200k.sim1.fq Ec200k.sim2.fq

gi|49175990|ref|NC_000913.2|	520	C	G	-
gi|49175990|ref|NC_000913.2|	1188	T	C	-
gi|49175990|ref|NC_000913.2|	1971	T	A	-
gi|49175990|ref|NC_000913.2|	4002	-	CC	-
gi|49175990|ref|NC_000913.2|	4710	T	C	-
gi|49175990|ref|NC_000913.2|	5007	T	C	-
gi|49175990|ref|NC_000913.2|	5756	C	G	-
gi|49175990|ref|NC_000913.2|	5897	A	C	-
gi|49175990|ref|NC_000913.2|	8041	T	C	-
gi|49175990|ref|NC_000913.2|	8678	A	G	-
gi|49175990|ref|NC_000913.2|	10251	T	C	-
gi|49175990|ref|NC_000913.2|	12023	T	G	-
gi|49175990|ref|NC_000913.2|	12453	T	A	-
gi|49175990|ref|NC_000913.2|	16446	C	T	-
gi|49175990|ref|NC_000913.2|	16626	T	A	-
gi|49175990|ref|NC_000913.2|	16765	A	C	-
gi|49175990|ref|NC_000913.2|	17739	T	C	-
gi|49175990|ref|NC_000913.2|	19560	G	A	-
gi|49175990|ref|NC_000913.2|	19778	A	C	-
gi|49175990|ref|NC_000913.2|	20663	T	C	-
gi|49175990|ref|NC_000913.2|	21532	A	T	-
gi|49175990|ref|NC_000913.2|	22226	G	A	-
gi|49175990|ref|NC_000913.2|	22860	T	G	-
gi|49175990|ref|NC_000913.2|	23553	A	G	-
gi|49175990|ref|NC_000913.2|	24068	C	A	-
gi|49175990|ref|NC_000913.2|	26338	T	C	-
gi|49175990|ref|NC_000913.2|	26792	T	C	-
gi|49175990|ref|NC_000913.2|	27554	G	A	-
gi|49175990|ref|NC_000913.2|	28009	C	G	-
gi|49175990|ref|NC_000913.2|	29147	A	T	-
gi|49175990|ref|NC_000913.2|	29719	A	C	-
gi|49175990|ref|NC_000913.2|	29955	T	C	-
gi|49175990|ref|NC_000913.2|	30538	G	T	-
gi|49175990|ref|NC_000913.2|	31957	G	C	-
gi|49175990|ref|NC_000913.2|	34943	A	G	-
gi|49175990|ref|NC_000913.2|	35409	C	T	-
gi|49175990|ref|NC_000913.2|	38238	T	A	-
gi|49175990|ref|NC_000913.2|	40568	A	-	-
gi|49175990|ref|NC_000913.2|	42996	G	C	-
gi|49175990|ref|NC_000913.2|	44615	G	T	-
gi|49175990|ref|NC_000913.2|	45845	C	A	-
gi|49175990|ref|NC_000913.2|	47879	C	T	-
gi|49175990|ref|NC_000913.2|	49274	C	T	-
gi|49175990|ref|NC_000913.2|	49662	T	G	-
gi|49175990|ref|NC_000913.2|	51554	G	C	-
gi|49175990|ref|NC_000913.2|	53309	A	C	-
gi|49175990|ref|NC_000913.2|	54364	C	G	-
gi|49175990|ref|NC_000913.2|	54873	G	C	-
gi|49175990|ref|NC_000913.2|	55615	T	C	-
gi|49175990|ref|NC_000913.2|	56236	G	C	-
gi|49175990|ref|NC_000913.2|	56531	T	G	-
gi|49175990|ref|NC_000913.2|	58571	T	G	-
gi|49175990|ref|NC_000913.2|	58897	T	C	-
gi|49175990|ref|NC_000913.2|	58899	G	A	-
gi|49175990|ref|NC_000913.2|	59447	-	G	-
gi|49175990|ref|NC_000913.2|	60510	A	C	-
gi|49175990|ref|NC_000913.2|	61594	T	A	-
gi|49175990|ref|NC_000913.2|	61878	G	A	-
gi|49175990|ref|NC_000913.2|	61890	-	GG	-
gi|49175990|ref|NC_000913.2|	62423	T	A	-
gi|49175990|ref|NC_000913.2|	62582	G	T	-
gi|49175990|ref|NC_000913.2|	62904	C	-	-
gi|49175990|ref|NC_000913.2|	62905	A	-	-
gi|49175990|ref|NC_000913.2|	62906	A	-	-
gi|49175990|ref|NC_000913.2|	63747	C	A	-
gi|49175990|ref|NC_000913.2|	66908	T	A	-
gi|49175990|ref|NC_000913.2|	66991	G	T	-
gi|49175990|ref|NC_000913.2|	67525	G	T	-
gi|49175990|ref|NC_000913.2|	69411	C	T	-
gi|49175990|ref|NC_000913.2|	69519	C	A	-
gi|49175990|ref|NC_000913.2|	70121	C	T	-
gi|49175990|ref|NC_000913.2|	71142	T	G	-
gi|49175990|ref|NC_000913.2|	71143	G	A	-
gi|49175990|ref|NC_000913.2|	71616	-	C	-
gi|49175990|ref|NC_000913.2|	73144	G	T	-
gi|49175990|ref|NC_000913.2|	75069	G	T	-
gi|49175990|ref|NC_000913.2|	76009	C	G	-
gi|49175990|ref|NC_000913.2|	77141	C	G	-
gi|49175990|ref|NC_000913.2|	77533	T	C	-
gi|49175990|ref|NC_000913.2|	80712	T	G	-
gi|49175990|ref|NC_000913.2|	81621	A	G	-
gi|49175990|ref|NC_000913.2|	82854	C	G	-
gi|49175990|ref|NC_000913.2|	83481	G	C	-
gi|49175990|ref|NC_000913.2|	83889	A	C	-
gi|49175990|ref|NC_000913.2|	84066	T	-	-
gi|49175990|ref|NC_000913.2|	85228	T	C	-
gi|49175990|ref|NC_000913.2|	85928	C	G	-
gi|49175990|ref|NC_000913.2|	86026	A	T	-
gi|49175990|ref|NC_000913.2|	86252	A	G	-
gi|49175990|ref|NC_000913.2|	86318	T	A	-
gi|49175990|ref|NC_000913.2|	88754	T	C	-
gi|49175990|ref|NC_000913.2|	89508	G	-	-
gi|49175990|ref|NC_000913.2|	90048	G	C	-
gi|49175990|ref|NC_000913.2|	90778	G	T	-
gi|49175990|ref|NC_000913.2|	91172	T	G	-
gi|49175990|ref|NC_000913.2|	93346	G	T	-
gi|49175990|ref|NC_000913.2|	94576	T	G	-
gi|49175990|ref|NC_000913.2|	96125	C	T	-
gi|49175990|ref|NC_000913.2|	98106	G	A	-
gi|49175990|ref|NC_000913.2|	100909	T	G	-
gi|49175990|ref|NC_000913.2|	101143	A	T	-
gi|49175990|ref|NC_000913.2|	101593	C	T	-
gi|49175990|ref|NC_000913.2|	101724	C	G	-
gi|49175990|ref|NC_000913.2|	101967	T	A	-
gi|49175990|ref|NC_000913.2|	102194	A	C	-
gi|49175990|ref|NC_000913.2|	103554	G	T	-
gi|49175990|ref|NC_000913.2|	105346	A	C	-
gi|49175990|ref|NC_000913.2|	107176	G	A	-
gi|49175990|ref|NC_000913.2|	108067	G	T	-
gi|49175990|ref|NC_000913.2|	109005	A	T	-
gi|49175990|ref|NC_000913.2|	109178	T	A	-
gi|49175990|ref|NC_000913.2|	111820	G	T	-
gi|49175990|ref|NC_000913.2|	112024	C	A	-
gi|49175990|ref|NC_000913.2|	112146	T	C	-
gi|49175990|ref|NC_000913.2|	112898	C	T	-
gi|49175990|ref|NC_000913.2|	113762	G	A	-
gi|49175990|ref|NC_000913.2|	114070	G	C	-
gi|49175990|ref|NC_000913.2|	115267	C	T	-
gi|49175990|ref|NC_000913.2|	116673	G	A	-
gi|49175990|ref|NC_000913.2|	118829	G	T	-
gi|49175990|ref|NC_000913.2|	119211	A	C	-
gi|49175990|ref|NC_000913.2|	119614	G	C	-
gi|49175990|ref|NC_000913.2|	124192	T	G	-
gi|49175990|ref|NC_000913.2|	124271	C	G	-
gi|49175990|ref|NC_000913.2|	124607	G	C	-
gi|49175990|ref|NC_000913.2|	125305	C	A	-
gi|49175990|ref|NC_000913.2|	127026	G	-	-
gi|49175990|ref|NC_000913.2|	127027	A	-	-
gi|49175990|ref|NC_000913.2|	127028	A	-	-
gi|49175990|ref|NC_000913.2|	127059	G	A	-
gi|49175990|ref|NC_000913.2|	128831	A	G	-
gi|49175990|ref|NC_000913.2|	132973	C	G	-
gi|49175990|ref|NC_000913.2|	134036	G	T	-
gi|49175990|ref|NC_000913.2|	135129	G	A	-
gi|49175990|ref|NC_000913.2|	135905	A	T	-
gi|49175990|ref|NC_000913.2|	136509	C	A	-
gi|49175990|ref|NC_000913.2|	136822	G	T	-
gi|49175990|ref|NC_000913.2|	137765	G	A	-
gi|49175990|ref|NC_000913.2|	138829	C	A	-
gi|49175990|ref|NC_000913.2|	140089	A	G	-
gi|49175990|ref|NC_000913.2|	142896	A	C	-
gi|49175990|ref|NC_000913.2|	143393	T	A	-
gi|49175990|ref|NC_000913.2|	143764	G	T	-
gi|49175990|ref|NC_000913.2|	143848	T	G	-
gi|49175990|ref|NC_000913.2|	143936	G	T	-
gi|49175990|ref|NC_000913.2|	145868	T	G	-
gi|49175990|ref|NC_000913.2|	149615	A	T	-
gi|49175990|ref|NC_000913.2|	150140	C	A	-
gi|49175990|ref|NC_000913.2|	150977	G	C	-
gi|49175990|ref|NC_000913.2|	153095	A	G	-
gi|49175990|ref|NC_000913.2|	154797	T	A	-
gi|49175990|ref|NC_000913.2|	156562	T	A	-
gi|49175990|ref|NC_000913.2|	159318	C	G	-
gi|49175990|ref|NC_000913.2|	159408	T	G	-
gi|49175990|ref|NC_000913.2|	160795	G	-	-
gi|49175990|ref|NC_000913.2|	160924	A	C	-
gi|49175990|ref|NC_000913.2|	161087	T	A	-
gi|49175990|ref|NC_000913.2|	161500	G	T	-
gi|49175990|ref|NC_000913.2|	162174	T	C	-
gi|49175990|ref|NC_000913.2|	162429	C	T	-
gi|49175990|ref|NC_000913.2|	163214	C	G	-
gi|49175990|ref|NC_000913.2|	163574	G	T	-
gi|49175990|ref|NC_000913.2|	163736	G	T	-
gi|49175990|ref|NC_000913.2|	164151	A	C	-
gi|49175990|ref|NC_000913.2|	164521	A	T	-
gi|49175990|ref|NC_000913.2|	164945	G	A	-
gi|49175990|ref|NC_000913.2|	166630	G	C	-
gi|49175990|ref|NC_000913.2|	167635	A	T	-
gi|49175990|ref|NC_000913.2|	168910	A	G	-
gi|49175990|ref|NC_000913.2|	169601	C	A	-
gi|49175990|ref|NC_000913.2|	170018	A	C	-
gi|49175990|ref|NC_000913.2|	171135	T	C	-
gi|49175990|ref|NC_000913.2|	171153	A	G	-
gi|49175990|ref|NC_000913.2|	171637	T	C	-
gi|49175990|ref|NC_000913.2|	172475	T	G	-
gi|49175990|ref|NC_000913.2|	172544	T	C	-
gi|49175990|ref|NC_000913.2|	174454	A	T	-
gi|49175990|ref|NC_000913.2|	175140	C	G	-
gi|49175990|ref|NC_000913.2|	176135	C	T	-
gi|49175990|ref|NC_000913.2|	177775	C	T	-
gi|49175990|ref|NC_000913.2|	178554	A	-	-
gi|49175990|ref|NC_000913.2|	178845	C	G	-
gi|49175990|ref|NC_000913.2|	181351	A	C	-
gi|49175990|ref|NC_000913.2|	181446	A	T	-
gi|49175990|ref|NC_000913.2|	185362	C	G	-
gi|49175990|ref|NC_000913.2|	185417	G	A	-
gi|49175990|ref|NC_000913.2|	186586	G	C	-
gi|49175990|ref|NC_000913.2|	188610	G	C	-
gi|49175990|ref|NC_000913.2|	191207	A	G	-
gi|49175990|ref|NC_000913.2|	192559	A	T	-
gi|49175990|ref|NC_000913.2|	193287	T	C	-
gi|49175990|ref|NC_000913.2|	195455	G	C	-
gi|49175990|ref|NC_000913.2|	195986	C	T	-
gi|49175990|ref|NC_000913.2|	199213	G	A	-



../src/preprocessor.pl Ec200k.sim1.fq | cut -f 12- -d'_' > Ec200k.sim1.sfa
../src/preprocessor.pl Ec200k.sim2.fq | cut -f 12- -d'_' > Ec200k.sim2.sfa
cat Ec200k.sim[12].sfa > Ec200k.sim.sfa




## Ec500k.sim.sfa
###############################################################################

~/build/samtools-0.1.6/misc/wgsim -h -d 210 -s 21 -N 500000 -1 36 -2 36 Ecoli.500k.fa Ec500k.sim1.fq Ec500k.sim2.fq

gi|49175990|ref|NC_000913.2|	767	A	T	-
gi|49175990|ref|NC_000913.2|	885	C	A	-
gi|49175990|ref|NC_000913.2|	1661	T	C	-
gi|49175990|ref|NC_000913.2|	2850	T	A	-
gi|49175990|ref|NC_000913.2|	3181	G	A	-
gi|49175990|ref|NC_000913.2|	3218	T	C	-
gi|49175990|ref|NC_000913.2|	3514	A	T	-
gi|49175990|ref|NC_000913.2|	3831	A	G	-
gi|49175990|ref|NC_000913.2|	3897	G	A	-
gi|49175990|ref|NC_000913.2|	5648	A	C	-
gi|49175990|ref|NC_000913.2|	6095	T	G	-
gi|49175990|ref|NC_000913.2|	7978	C	A	-
gi|49175990|ref|NC_000913.2|	10264	C	-	-
gi|49175990|ref|NC_000913.2|	10301	C	G	-
gi|49175990|ref|NC_000913.2|	13066	C	G	-
gi|49175990|ref|NC_000913.2|	15324	A	C	-
gi|49175990|ref|NC_000913.2|	15701	A	T	-
gi|49175990|ref|NC_000913.2|	15876	T	A	-
gi|49175990|ref|NC_000913.2|	17286	C	A	-
gi|49175990|ref|NC_000913.2|	17570	A	G	-
gi|49175990|ref|NC_000913.2|	19664	G	A	-
gi|49175990|ref|NC_000913.2|	20508	C	-	-
gi|49175990|ref|NC_000913.2|	21163	T	A	-
gi|49175990|ref|NC_000913.2|	21317	A	C	-
gi|49175990|ref|NC_000913.2|	22157	G	A	-
gi|49175990|ref|NC_000913.2|	22641	T	C	-
gi|49175990|ref|NC_000913.2|	23526	C	A	-
gi|49175990|ref|NC_000913.2|	24915	T	G	-
gi|49175990|ref|NC_000913.2|	25444	A	-	-
gi|49175990|ref|NC_000913.2|	27792	C	A	-
gi|49175990|ref|NC_000913.2|	28299	G	A	-
gi|49175990|ref|NC_000913.2|	31869	C	T	-
gi|49175990|ref|NC_000913.2|	32856	T	G	-
gi|49175990|ref|NC_000913.2|	32966	C	G	-
gi|49175990|ref|NC_000913.2|	35697	T	G	-
gi|49175990|ref|NC_000913.2|	36153	A	-	-
gi|49175990|ref|NC_000913.2|	36154	T	-	-
gi|49175990|ref|NC_000913.2|	36245	G	T	-
gi|49175990|ref|NC_000913.2|	39752	A	C	-
gi|49175990|ref|NC_000913.2|	40690	G	C	-
gi|49175990|ref|NC_000913.2|	42907	A	G	-
gi|49175990|ref|NC_000913.2|	43233	C	T	-
gi|49175990|ref|NC_000913.2|	44063	G	T	-
gi|49175990|ref|NC_000913.2|	44803	G	C	-
gi|49175990|ref|NC_000913.2|	45636	C	A	-
gi|49175990|ref|NC_000913.2|	46419	C	A	-
gi|49175990|ref|NC_000913.2|	47254	T	A	-
gi|49175990|ref|NC_000913.2|	47796	C	G	-
gi|49175990|ref|NC_000913.2|	48003	C	A	-
gi|49175990|ref|NC_000913.2|	51360	T	A	-
gi|49175990|ref|NC_000913.2|	51769	C	G	-
gi|49175990|ref|NC_000913.2|	52407	G	C	-
gi|49175990|ref|NC_000913.2|	54863	G	C	-
gi|49175990|ref|NC_000913.2|	55434	G	C	-
gi|49175990|ref|NC_000913.2|	55585	C	T	-
gi|49175990|ref|NC_000913.2|	55893	A	C	-
gi|49175990|ref|NC_000913.2|	56590	G	T	-
gi|49175990|ref|NC_000913.2|	57578	T	C	-
gi|49175990|ref|NC_000913.2|	57769	C	A	-
gi|49175990|ref|NC_000913.2|	58966	A	T	-
gi|49175990|ref|NC_000913.2|	61356	G	A	-
gi|49175990|ref|NC_000913.2|	61804	G	A	-
gi|49175990|ref|NC_000913.2|	62033	T	G	-
gi|49175990|ref|NC_000913.2|	64378	T	-	-
gi|49175990|ref|NC_000913.2|	65749	T	G	-
gi|49175990|ref|NC_000913.2|	66202	T	C	-
gi|49175990|ref|NC_000913.2|	67794	C	T	-
gi|49175990|ref|NC_000913.2|	68931	T	G	-
gi|49175990|ref|NC_000913.2|	69274	G	A	-
gi|49175990|ref|NC_000913.2|	70573	G	T	-
gi|49175990|ref|NC_000913.2|	70721	C	T	-
gi|49175990|ref|NC_000913.2|	72598	C	G	-
gi|49175990|ref|NC_000913.2|	72809	G	A	-
gi|49175990|ref|NC_000913.2|	73472	C	T	-
gi|49175990|ref|NC_000913.2|	77617	A	T	-
gi|49175990|ref|NC_000913.2|	80180	T	G	-
gi|49175990|ref|NC_000913.2|	80731	C	T	-
gi|49175990|ref|NC_000913.2|	81336	A	T	-
gi|49175990|ref|NC_000913.2|	81371	G	T	-
gi|49175990|ref|NC_000913.2|	81373	C	A	-
gi|49175990|ref|NC_000913.2|	82946	T	G	-
gi|49175990|ref|NC_000913.2|	85035	G	C	-
gi|49175990|ref|NC_000913.2|	86674	G	T	-
gi|49175990|ref|NC_000913.2|	89290	C	G	-
gi|49175990|ref|NC_000913.2|	91143	C	A	-
gi|49175990|ref|NC_000913.2|	92740	C	T	-
gi|49175990|ref|NC_000913.2|	94063	G	C	-
gi|49175990|ref|NC_000913.2|	94472	G	T	-
gi|49175990|ref|NC_000913.2|	94768	T	C	-
gi|49175990|ref|NC_000913.2|	96037	T	A	-
gi|49175990|ref|NC_000913.2|	97586	C	A	-
gi|49175990|ref|NC_000913.2|	99552	T	A	-
gi|49175990|ref|NC_000913.2|	101804	T	G	-
gi|49175990|ref|NC_000913.2|	102548	G	C	-
gi|49175990|ref|NC_000913.2|	103143	T	G	-
gi|49175990|ref|NC_000913.2|	103937	A	T	-
gi|49175990|ref|NC_000913.2|	105151	T	A	-
gi|49175990|ref|NC_000913.2|	108017	G	T	-
gi|49175990|ref|NC_000913.2|	108543	C	A	-
gi|49175990|ref|NC_000913.2|	109034	A	T	-
gi|49175990|ref|NC_000913.2|	115638	A	G	-
gi|49175990|ref|NC_000913.2|	116471	G	-	-
gi|49175990|ref|NC_000913.2|	117559	T	A	-
gi|49175990|ref|NC_000913.2|	118220	C	G	-
gi|49175990|ref|NC_000913.2|	118401	G	C	-
gi|49175990|ref|NC_000913.2|	118569	G	C	-
gi|49175990|ref|NC_000913.2|	120484	C	G	-
gi|49175990|ref|NC_000913.2|	120829	A	G	-
gi|49175990|ref|NC_000913.2|	122747	A	G	-
gi|49175990|ref|NC_000913.2|	126776	T	-	-
gi|49175990|ref|NC_000913.2|	126777	T	-	-
gi|49175990|ref|NC_000913.2|	127981	C	T	-
gi|49175990|ref|NC_000913.2|	127992	T	-	-
gi|49175990|ref|NC_000913.2|	127993	T	-	-
gi|49175990|ref|NC_000913.2|	128887	C	G	-
gi|49175990|ref|NC_000913.2|	130606	T	A	-
gi|49175990|ref|NC_000913.2|	134837	C	G	-
gi|49175990|ref|NC_000913.2|	135703	A	T	-
gi|49175990|ref|NC_000913.2|	136775	T	G	-
gi|49175990|ref|NC_000913.2|	137024	G	C	-
gi|49175990|ref|NC_000913.2|	138738	C	T	-
gi|49175990|ref|NC_000913.2|	139618	G	-	-
gi|49175990|ref|NC_000913.2|	140180	G	A	-
gi|49175990|ref|NC_000913.2|	140355	T	C	-
gi|49175990|ref|NC_000913.2|	140921	A	C	-
gi|49175990|ref|NC_000913.2|	141972	G	A	-
gi|49175990|ref|NC_000913.2|	144786	G	T	-
gi|49175990|ref|NC_000913.2|	145196	G	C	-
gi|49175990|ref|NC_000913.2|	145491	T	G	-
gi|49175990|ref|NC_000913.2|	147396	G	A	-
gi|49175990|ref|NC_000913.2|	153008	T	C	-
gi|49175990|ref|NC_000913.2|	154510	A	G	-
gi|49175990|ref|NC_000913.2|	154802	C	T	-
gi|49175990|ref|NC_000913.2|	156664	C	G	-
gi|49175990|ref|NC_000913.2|	157174	T	G	-
gi|49175990|ref|NC_000913.2|	157223	G	A	-
gi|49175990|ref|NC_000913.2|	157672	C	G	-
gi|49175990|ref|NC_000913.2|	158095	A	G	-
gi|49175990|ref|NC_000913.2|	158118	T	C	-
gi|49175990|ref|NC_000913.2|	159054	C	G	-
gi|49175990|ref|NC_000913.2|	159157	A	G	-
gi|49175990|ref|NC_000913.2|	162831	T	G	-
gi|49175990|ref|NC_000913.2|	164550	T	A	-
gi|49175990|ref|NC_000913.2|	165453	G	C	-
gi|49175990|ref|NC_000913.2|	165640	A	T	-
gi|49175990|ref|NC_000913.2|	167056	G	C	-
gi|49175990|ref|NC_000913.2|	168466	C	-	-
gi|49175990|ref|NC_000913.2|	170033	-	T	-
gi|49175990|ref|NC_000913.2|	170674	G	A	-
gi|49175990|ref|NC_000913.2|	173205	A	C	-
gi|49175990|ref|NC_000913.2|	173417	C	T	-
gi|49175990|ref|NC_000913.2|	175893	G	T	-
gi|49175990|ref|NC_000913.2|	175985	A	T	-
gi|49175990|ref|NC_000913.2|	176868	A	T	-
gi|49175990|ref|NC_000913.2|	177526	C	A	-
gi|49175990|ref|NC_000913.2|	177588	C	A	-
gi|49175990|ref|NC_000913.2|	178193	G	C	-
gi|49175990|ref|NC_000913.2|	182133	A	C	-
gi|49175990|ref|NC_000913.2|	184633	A	-	-
gi|49175990|ref|NC_000913.2|	184885	A	T	-
gi|49175990|ref|NC_000913.2|	186272	G	A	-
gi|49175990|ref|NC_000913.2|	186437	T	C	-
gi|49175990|ref|NC_000913.2|	187695	A	C	-
gi|49175990|ref|NC_000913.2|	188768	T	G	-
gi|49175990|ref|NC_000913.2|	189981	C	T	-
gi|49175990|ref|NC_000913.2|	191923	C	A	-
gi|49175990|ref|NC_000913.2|	192008	G	A	-
gi|49175990|ref|NC_000913.2|	193171	T	A	-
gi|49175990|ref|NC_000913.2|	195831	G	A	-
gi|49175990|ref|NC_000913.2|	197429	A	T	-
gi|49175990|ref|NC_000913.2|	197551	C	A	-
gi|49175990|ref|NC_000913.2|	197786	T	A	-
gi|49175990|ref|NC_000913.2|	200029	A	T	-
gi|49175990|ref|NC_000913.2|	200554	G	A	-
gi|49175990|ref|NC_000913.2|	200903	C	T	-
gi|49175990|ref|NC_000913.2|	203235	G	T	-
gi|49175990|ref|NC_000913.2|	203563	G	-	-
gi|49175990|ref|NC_000913.2|	203564	C	-	-
gi|49175990|ref|NC_000913.2|	205980	C	-	-
gi|49175990|ref|NC_000913.2|	205981	A	-	-
gi|49175990|ref|NC_000913.2|	206239	T	-	-
gi|49175990|ref|NC_000913.2|	206966	G	T	-
gi|49175990|ref|NC_000913.2|	208334	T	A	-
gi|49175990|ref|NC_000913.2|	208599	G	T	-
gi|49175990|ref|NC_000913.2|	209252	T	C	-
gi|49175990|ref|NC_000913.2|	209828	T	G	-
gi|49175990|ref|NC_000913.2|	209829	C	G	-
gi|49175990|ref|NC_000913.2|	210082	C	-	-
gi|49175990|ref|NC_000913.2|	210876	T	A	-
gi|49175990|ref|NC_000913.2|	211072	G	C	-
gi|49175990|ref|NC_000913.2|	213108	C	T	-
gi|49175990|ref|NC_000913.2|	213824	G	A	-
gi|49175990|ref|NC_000913.2|	215002	T	A	-
gi|49175990|ref|NC_000913.2|	216906	G	A	-
gi|49175990|ref|NC_000913.2|	217545	C	-	-
gi|49175990|ref|NC_000913.2|	218409	T	C	-
gi|49175990|ref|NC_000913.2|	218897	T	A	-
gi|49175990|ref|NC_000913.2|	219573	G	A	-
gi|49175990|ref|NC_000913.2|	221812	G	A	-
gi|49175990|ref|NC_000913.2|	223775	T	A	-
gi|49175990|ref|NC_000913.2|	225460	T	G	-
gi|49175990|ref|NC_000913.2|	227347	T	A	-
gi|49175990|ref|NC_000913.2|	228861	G	C	-
gi|49175990|ref|NC_000913.2|	229636	C	A	-
gi|49175990|ref|NC_000913.2|	231155	G	C	-
gi|49175990|ref|NC_000913.2|	232881	C	A	-
gi|49175990|ref|NC_000913.2|	233067	G	A	-
gi|49175990|ref|NC_000913.2|	235400	G	A	-
gi|49175990|ref|NC_000913.2|	235842	A	G	-
gi|49175990|ref|NC_000913.2|	236289	G	A	-
gi|49175990|ref|NC_000913.2|	236405	G	A	-
gi|49175990|ref|NC_000913.2|	236783	C	T	-
gi|49175990|ref|NC_000913.2|	240868	T	A	-
gi|49175990|ref|NC_000913.2|	240989	T	A	-
gi|49175990|ref|NC_000913.2|	242174	G	-	-
gi|49175990|ref|NC_000913.2|	242175	T	-	-
gi|49175990|ref|NC_000913.2|	242176	G	-	-
gi|49175990|ref|NC_000913.2|	242177	A	-	-
gi|49175990|ref|NC_000913.2|	242460	G	T	-
gi|49175990|ref|NC_000913.2|	242638	T	A	-
gi|49175990|ref|NC_000913.2|	243421	C	A	-
gi|49175990|ref|NC_000913.2|	245310	G	A	-
gi|49175990|ref|NC_000913.2|	245484	G	A	-
gi|49175990|ref|NC_000913.2|	246916	G	C	-
gi|49175990|ref|NC_000913.2|	248053	C	G	-
gi|49175990|ref|NC_000913.2|	248259	C	T	-
gi|49175990|ref|NC_000913.2|	248376	A	G	-
gi|49175990|ref|NC_000913.2|	248667	C	G	-
gi|49175990|ref|NC_000913.2|	248896	G	T	-
gi|49175990|ref|NC_000913.2|	251111	C	T	-
gi|49175990|ref|NC_000913.2|	252293	G	-	-
gi|49175990|ref|NC_000913.2|	254666	C	T	-
gi|49175990|ref|NC_000913.2|	255026	G	A	-
gi|49175990|ref|NC_000913.2|	256753	G	C	-
gi|49175990|ref|NC_000913.2|	258378	T	G	-
gi|49175990|ref|NC_000913.2|	259304	T	A	-
gi|49175990|ref|NC_000913.2|	259823	C	G	-
gi|49175990|ref|NC_000913.2|	260666	A	G	-
gi|49175990|ref|NC_000913.2|	262069	-	C	-
gi|49175990|ref|NC_000913.2|	262163	C	A	-
gi|49175990|ref|NC_000913.2|	262215	A	C	-
gi|49175990|ref|NC_000913.2|	263375	C	T	-
gi|49175990|ref|NC_000913.2|	265350	G	A	-
gi|49175990|ref|NC_000913.2|	265628	A	-	-
gi|49175990|ref|NC_000913.2|	265978	G	T	-
gi|49175990|ref|NC_000913.2|	266475	-	A	-
gi|49175990|ref|NC_000913.2|	267502	G	A	-
gi|49175990|ref|NC_000913.2|	268356	T	G	-
gi|49175990|ref|NC_000913.2|	270952	G	C	-
gi|49175990|ref|NC_000913.2|	271881	T	G	-
gi|49175990|ref|NC_000913.2|	272938	G	A	-
gi|49175990|ref|NC_000913.2|	273561	T	A	-
gi|49175990|ref|NC_000913.2|	274684	G	C	-
gi|49175990|ref|NC_000913.2|	280553	A	G	-
gi|49175990|ref|NC_000913.2|	280893	G	T	-
gi|49175990|ref|NC_000913.2|	282831	-	C	-
gi|49175990|ref|NC_000913.2|	283174	T	G	-
gi|49175990|ref|NC_000913.2|	284177	A	G	-
gi|49175990|ref|NC_000913.2|	284328	G	T	-
gi|49175990|ref|NC_000913.2|	284329	T	G	-
gi|49175990|ref|NC_000913.2|	286396	G	T	-
gi|49175990|ref|NC_000913.2|	288310	A	G	-
gi|49175990|ref|NC_000913.2|	288389	T	C	-
gi|49175990|ref|NC_000913.2|	289125	C	G	-
gi|49175990|ref|NC_000913.2|	289565	A	T	-
gi|49175990|ref|NC_000913.2|	289993	A	-	-
gi|49175990|ref|NC_000913.2|	292005	-	A	-
gi|49175990|ref|NC_000913.2|	292363	A	C	-
gi|49175990|ref|NC_000913.2|	292755	A	G	-
gi|49175990|ref|NC_000913.2|	293545	G	T	-
gi|49175990|ref|NC_000913.2|	293900	A	G	-
gi|49175990|ref|NC_000913.2|	294671	T	C	-
gi|49175990|ref|NC_000913.2|	297314	-	C	-
gi|49175990|ref|NC_000913.2|	298685	C	T	-
gi|49175990|ref|NC_000913.2|	298749	G	A	-
gi|49175990|ref|NC_000913.2|	300139	G	A	-
gi|49175990|ref|NC_000913.2|	302223	A	C	-
gi|49175990|ref|NC_000913.2|	302636	T	-	-
gi|49175990|ref|NC_000913.2|	303055	A	G	-
gi|49175990|ref|NC_000913.2|	303277	A	G	-
gi|49175990|ref|NC_000913.2|	303366	C	T	-
gi|49175990|ref|NC_000913.2|	303592	C	T	-
gi|49175990|ref|NC_000913.2|	304505	T	-	-
gi|49175990|ref|NC_000913.2|	304506	T	-	-
gi|49175990|ref|NC_000913.2|	304619	A	T	-
gi|49175990|ref|NC_000913.2|	304721	A	T	-
gi|49175990|ref|NC_000913.2|	309867	A	G	-
gi|49175990|ref|NC_000913.2|	310934	G	C	-
gi|49175990|ref|NC_000913.2|	311391	G	C	-
gi|49175990|ref|NC_000913.2|	312648	G	C	-
gi|49175990|ref|NC_000913.2|	313692	A	C	-
gi|49175990|ref|NC_000913.2|	314471	G	A	-
gi|49175990|ref|NC_000913.2|	315896	A	T	-
gi|49175990|ref|NC_000913.2|	317706	T	C	-
gi|49175990|ref|NC_000913.2|	317963	A	G	-
gi|49175990|ref|NC_000913.2|	318666	A	T	-
gi|49175990|ref|NC_000913.2|	323539	A	G	-
gi|49175990|ref|NC_000913.2|	324027	C	G	-
gi|49175990|ref|NC_000913.2|	325027	-	GG	-
gi|49175990|ref|NC_000913.2|	326473	T	A	-
gi|49175990|ref|NC_000913.2|	329073	A	T	-
gi|49175990|ref|NC_000913.2|	329169	C	T	-
gi|49175990|ref|NC_000913.2|	330260	T	A	-
gi|49175990|ref|NC_000913.2|	331131	A	C	-
gi|49175990|ref|NC_000913.2|	334033	C	T	-
gi|49175990|ref|NC_000913.2|	334348	C	G	-
gi|49175990|ref|NC_000913.2|	335079	T	C	-
gi|49175990|ref|NC_000913.2|	336474	T	A	-
gi|49175990|ref|NC_000913.2|	337153	C	A	-
gi|49175990|ref|NC_000913.2|	337398	T	A	-
gi|49175990|ref|NC_000913.2|	338151	-	TTT	-
gi|49175990|ref|NC_000913.2|	338235	A	G	-
gi|49175990|ref|NC_000913.2|	338570	T	G	-
gi|49175990|ref|NC_000913.2|	339594	A	C	-
gi|49175990|ref|NC_000913.2|	340304	C	A	-
gi|49175990|ref|NC_000913.2|	340404	C	G	-
gi|49175990|ref|NC_000913.2|	341698	A	G	-
gi|49175990|ref|NC_000913.2|	341959	G	C	-
gi|49175990|ref|NC_000913.2|	342670	A	C	-
gi|49175990|ref|NC_000913.2|	343020	G	T	-
gi|49175990|ref|NC_000913.2|	344073	T	C	-
gi|49175990|ref|NC_000913.2|	344281	T	A	-
gi|49175990|ref|NC_000913.2|	344936	-	G	-
gi|49175990|ref|NC_000913.2|	347318	-	TT	-
gi|49175990|ref|NC_000913.2|	348555	C	G	-
gi|49175990|ref|NC_000913.2|	348752	G	A	-
gi|49175990|ref|NC_000913.2|	349679	T	-	-
gi|49175990|ref|NC_000913.2|	349845	G	T	-
gi|49175990|ref|NC_000913.2|	351120	G	A	-
gi|49175990|ref|NC_000913.2|	351443	A	C	-
gi|49175990|ref|NC_000913.2|	351685	G	A	-
gi|49175990|ref|NC_000913.2|	351697	T	G	-
gi|49175990|ref|NC_000913.2|	357234	A	T	-
gi|49175990|ref|NC_000913.2|	358917	G	A	-
gi|49175990|ref|NC_000913.2|	362008	G	T	-
gi|49175990|ref|NC_000913.2|	363710	A	T	-
gi|49175990|ref|NC_000913.2|	365847	C	A	-
gi|49175990|ref|NC_000913.2|	366307	A	G	-
gi|49175990|ref|NC_000913.2|	369188	C	A	-
gi|49175990|ref|NC_000913.2|	369420	G	C	-
gi|49175990|ref|NC_000913.2|	370232	G	C	-
gi|49175990|ref|NC_000913.2|	371442	C	G	-
gi|49175990|ref|NC_000913.2|	371780	T	G	-
gi|49175990|ref|NC_000913.2|	372716	G	T	-
gi|49175990|ref|NC_000913.2|	373923	G	C	-
gi|49175990|ref|NC_000913.2|	374241	A	G	-
gi|49175990|ref|NC_000913.2|	374592	-	A	-
gi|49175990|ref|NC_000913.2|	375954	G	T	-
gi|49175990|ref|NC_000913.2|	379644	C	G	-
gi|49175990|ref|NC_000913.2|	380448	T	G	-
gi|49175990|ref|NC_000913.2|	381262	T	G	-
gi|49175990|ref|NC_000913.2|	381299	C	T	-
gi|49175990|ref|NC_000913.2|	382670	C	T	-
gi|49175990|ref|NC_000913.2|	384234	A	G	-
gi|49175990|ref|NC_000913.2|	385254	G	T	-
gi|49175990|ref|NC_000913.2|	385256	G	A	-
gi|49175990|ref|NC_000913.2|	385356	G	T	-
gi|49175990|ref|NC_000913.2|	385852	G	C	-
gi|49175990|ref|NC_000913.2|	386521	T	G	-
gi|49175990|ref|NC_000913.2|	387131	C	G	-
gi|49175990|ref|NC_000913.2|	387690	T	-	-
gi|49175990|ref|NC_000913.2|	388144	A	C	-
gi|49175990|ref|NC_000913.2|	390987	T	G	-
gi|49175990|ref|NC_000913.2|	392436	T	G	-
gi|49175990|ref|NC_000913.2|	392725	C	A	-
gi|49175990|ref|NC_000913.2|	394053	A	G	-
gi|49175990|ref|NC_000913.2|	395577	A	C	-
gi|49175990|ref|NC_000913.2|	396201	G	C	-
gi|49175990|ref|NC_000913.2|	397592	G	C	-
gi|49175990|ref|NC_000913.2|	397711	C	G	-
gi|49175990|ref|NC_000913.2|	399731	C	T	-
gi|49175990|ref|NC_000913.2|	401353	C	G	-
gi|49175990|ref|NC_000913.2|	401570	-	T	-
gi|49175990|ref|NC_000913.2|	402048	-	C	-
gi|49175990|ref|NC_000913.2|	402931	T	C	-
gi|49175990|ref|NC_000913.2|	403078	G	T	-
gi|49175990|ref|NC_000913.2|	403489	T	A	-
gi|49175990|ref|NC_000913.2|	404024	C	G	-
gi|49175990|ref|NC_000913.2|	404653	T	G	-
gi|49175990|ref|NC_000913.2|	404923	A	-	-
gi|49175990|ref|NC_000913.2|	405442	G	A	-
gi|49175990|ref|NC_000913.2|	407968	A	T	-
gi|49175990|ref|NC_000913.2|	409274	A	C	-
gi|49175990|ref|NC_000913.2|	410442	A	C	-
gi|49175990|ref|NC_000913.2|	410879	A	T	-
gi|49175990|ref|NC_000913.2|	411064	A	G	-
gi|49175990|ref|NC_000913.2|	411632	-	CCC	-
gi|49175990|ref|NC_000913.2|	412770	T	A	-
gi|49175990|ref|NC_000913.2|	415302	T	C	-
gi|49175990|ref|NC_000913.2|	415494	A	G	-
gi|49175990|ref|NC_000913.2|	419699	A	T	-
gi|49175990|ref|NC_000913.2|	419879	T	C	-
gi|49175990|ref|NC_000913.2|	420781	-	A	-
gi|49175990|ref|NC_000913.2|	422517	T	A	-
gi|49175990|ref|NC_000913.2|	423232	A	C	-
gi|49175990|ref|NC_000913.2|	423982	T	G	-
gi|49175990|ref|NC_000913.2|	424220	G	C	-
gi|49175990|ref|NC_000913.2|	426379	G	T	-
gi|49175990|ref|NC_000913.2|	426605	-	T	-
gi|49175990|ref|NC_000913.2|	426763	C	G	-
gi|49175990|ref|NC_000913.2|	428605	G	C	-
gi|49175990|ref|NC_000913.2|	429252	T	G	-
gi|49175990|ref|NC_000913.2|	431295	C	T	-
gi|49175990|ref|NC_000913.2|	432589	G	A	-
gi|49175990|ref|NC_000913.2|	434058	C	T	-
gi|49175990|ref|NC_000913.2|	434066	G	C	-
gi|49175990|ref|NC_000913.2|	438046	G	A	-
gi|49175990|ref|NC_000913.2|	438683	C	T	-
gi|49175990|ref|NC_000913.2|	439321	A	G	-
gi|49175990|ref|NC_000913.2|	439475	G	C	-
gi|49175990|ref|NC_000913.2|	440168	T	A	-
gi|49175990|ref|NC_000913.2|	440439	C	G	-
gi|49175990|ref|NC_000913.2|	440500	G	C	-
gi|49175990|ref|NC_000913.2|	441145	G	C	-
gi|49175990|ref|NC_000913.2|	441342	C	A	-
gi|49175990|ref|NC_000913.2|	442387	G	T	-
gi|49175990|ref|NC_000913.2|	444756	C	A	-
gi|49175990|ref|NC_000913.2|	445205	A	T	-
gi|49175990|ref|NC_000913.2|	448270	G	T	-
gi|49175990|ref|NC_000913.2|	448947	G	C	-
gi|49175990|ref|NC_000913.2|	449614	A	C	-
gi|49175990|ref|NC_000913.2|	450324	T	G	-
gi|49175990|ref|NC_000913.2|	452894	A	G	-
gi|49175990|ref|NC_000913.2|	453839	T	A	-
gi|49175990|ref|NC_000913.2|	454103	T	C	-
gi|49175990|ref|NC_000913.2|	454934	G	T	-
gi|49175990|ref|NC_000913.2|	456084	C	A	-
gi|49175990|ref|NC_000913.2|	459187	G	A	-
gi|49175990|ref|NC_000913.2|	459221	C	A	-
gi|49175990|ref|NC_000913.2|	459259	G	-	-
gi|49175990|ref|NC_000913.2|	459801	-	C	-
gi|49175990|ref|NC_000913.2|	460063	-	C	-
gi|49175990|ref|NC_000913.2|	461315	C	A	-
gi|49175990|ref|NC_000913.2|	461409	G	A	-
gi|49175990|ref|NC_000913.2|	461549	C	A	-
gi|49175990|ref|NC_000913.2|	462172	C	G	-
gi|49175990|ref|NC_000913.2|	462975	A	T	-
gi|49175990|ref|NC_000913.2|	462995	-	AA	-
gi|49175990|ref|NC_000913.2|	465695	A	G	-
gi|49175990|ref|NC_000913.2|	466192	T	G	-
gi|49175990|ref|NC_000913.2|	466835	G	-	-
gi|49175990|ref|NC_000913.2|	470556	G	A	-
gi|49175990|ref|NC_000913.2|	470821	T	C	-
gi|49175990|ref|NC_000913.2|	471288	C	T	-
gi|49175990|ref|NC_000913.2|	472587	C	A	-
gi|49175990|ref|NC_000913.2|	472712	C	T	-
gi|49175990|ref|NC_000913.2|	472834	T	C	-
gi|49175990|ref|NC_000913.2|	473743	G	-	-
gi|49175990|ref|NC_000913.2|	474059	C	A	-
gi|49175990|ref|NC_000913.2|	475326	G	A	-
gi|49175990|ref|NC_000913.2|	477878	-	T	-
gi|49175990|ref|NC_000913.2|	478790	A	G	-
gi|49175990|ref|NC_000913.2|	479709	T	A	-
gi|49175990|ref|NC_000913.2|	479877	T	G	-
gi|49175990|ref|NC_000913.2|	480111	A	C	-
gi|49175990|ref|NC_000913.2|	482370	T	G	-
gi|49175990|ref|NC_000913.2|	483545	A	G	-
gi|49175990|ref|NC_000913.2|	485224	A	T	-
gi|49175990|ref|NC_000913.2|	486052	C	A	-
gi|49175990|ref|NC_000913.2|	486179	G	A	-
gi|49175990|ref|NC_000913.2|	487241	G	T	-
gi|49175990|ref|NC_000913.2|	488047	A	T	-
gi|49175990|ref|NC_000913.2|	488364	G	C	-
gi|49175990|ref|NC_000913.2|	488658	C	T	-
gi|49175990|ref|NC_000913.2|	489562	A	T	-
gi|49175990|ref|NC_000913.2|	489977	-	GGG	-
gi|49175990|ref|NC_000913.2|	490768	A	C	-
gi|49175990|ref|NC_000913.2|	491132	G	T	-
gi|49175990|ref|NC_000913.2|	491954	C	T	-
gi|49175990|ref|NC_000913.2|	492423	G	C	-
gi|49175990|ref|NC_000913.2|	493440	C	T	-
gi|49175990|ref|NC_000913.2|	494250	A	G	-
gi|49175990|ref|NC_000913.2|	494771	C	G	-
gi|49175990|ref|NC_000913.2|	496384	A	T	-
gi|49175990|ref|NC_000913.2|	497790	C	T	-
gi|49175990|ref|NC_000913.2|	498240	A	T	-
gi|49175990|ref|NC_000913.2|	499310	-	GG	-
gi|49175990|ref|NC_000913.2|	499372	A	-	-
gi|49175990|ref|NC_000913.2|	499373	T	-	-




../src/preprocessor.pl Ec500k.sim1.fq | cut -f 12- -d'_' > Ec500k.sim1.sfa
../src/preprocessor.pl Ec500k.sim2.fq | cut -f 12- -d'_' > Ec500k.sim2.sfa
cat Ec500k.sim[12].sfa > Ec500k.sim.sfa

# Correct errors
~/build/packages/quake/bin/quake.py -f Ec500k.sim.fq.list -k 15
../src/preprocessor.pl Ec500k.sim1.cor.fq \
                       Ec500k.sim2.cor.fq \
                       Ec500k.sim1.cor_single.fq \
                       Ec500k.sim2.cor_single.fq \
              | cut -f 12- -d'_' > Ec500k.sim.cor.sfa

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