File: expected.txt

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ERR225922.R.3
	TAGGAGAGGCCTCGAGGGTGGAAAGGTCAGGAGAGTAGGGTTCGGCAGCAGCCCAGAGTGGGCATACAGCTGCAGG - aligned
	AGTTAAAATAAAAGTTAAATAAAAGTCCCTGCAGCTGTATGCCCACTCTGGTCTGCTGCCGAACCCTACTCTCCTG - aligned


ERR225922.R.4
	ATAGGCCACATAGGAGAGGCCTCGAGGGTGGAAAGGTCAAGAGAGTAGGGTTCGGCAGCAGCCCAGAGTGGGCATA - aligned
	TCATATAAAAGTCCCTGCAGCTGTATGCCCACTCTGGGCTGCTGCCGAACCCTACTCTCTTGACCTTTCCACCCTC - aligned


Read 2 spots for ERR225922
ERR225922.R.18536	CM000663.1	1649873	4M1D72M	TTATAATGGTCTGTGACACACGCACGCTTTCAGCTAGAGTTTGCTCTCTCTGGTTTTCGGTCTGTGATACACGCAC	aligned
ERR225922.R.3	CM000663.1	4546122	4M1D72M	AGTTAAAATAAAAGTTAAATAAAAGTCCCTGCAGCTGTATGCCCACTCTGGTCTGCTGCCGAACCCTACTCTCCTG	aligned
ERR225922.R.4	CM000663.1	4546137	76M	TCATATAAAAGTCCCTGCAGCTGTATGCCCACTCTGGGCTGCTGCCGAACCCTACTCTCTTGACCTTTCCACCCTC	aligned
ERR225922.R.3	CM000663.1	4546150	76M	TAGGAGAGGCCTCGAGGGTGGAAAGGTCAGGAGAGTAGGGTTCGGCAGCAGCCCAGAGTGGGCATACAGCTGCAGG	aligned
Read 4 alignments for ERR225922
SRR1121656.R.77	NC_000001.10	9999	1X89=1X10=	ATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAC
SRR1121656.R.36	NC_000001.10	9999	1X89=1X8=2S	ATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCGTAACCCTAAC
SRR1121656.R.2	NC_000001.10	9999	35S2X64=	CCCTACCCCTACCCCTAACCCTAACCCTACCCCTAACAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
SRR1121656.R.1	NC_000001.10	9999	1X22=1X25=52S	ATAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACAATAACCCTAACCCTAACACTAACCTTACCCCTAACCCTAACCCTCAC
SRR1121656.R.375469798	NC_000001.10	9999	1X34=66S	ATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCATAACCATAACACTAACCGAAACCCTACCCCACACCACACGCTGAAC
Read 5 alignments for SRR1121656
NC_000001.10	9999	N	0		
NC_000001.10	10000	N	5	^!A^!A^!a^!A^!A	&0#3#
NC_000001.10	10001	T	37	..c..^!.^!.^!.^!.^!.^!.^!.^!.^>.^*.^!.^>.^#.^!.^!.^!.^/.^>.^0.^2.^*.^-.^,.^0.^%.^0.^0.^2.^*.^+.^-.^-.	AAF.#CCCCC?C;;ICC?>?????G?H+=KEFDIGII
NC_000001.10	10002	A	67	..,..................................^*.^>.^!.^!.^!.^!.^!.^!.^!.^!.^>.^/.^!.^!.^!.^!.^>.^>.^-.^+.^>.^2.^-.^2.^>.^!.^5.^!.^!.^-.	89E:#BA?ABABBAFBBB@AAAAADAE?BJ>DAEFBF@CC?C?=/;CB??@D@CCBDB??????#8H
NC_000001.10	10003	A	96	..,................................................................^>.^!.^!.^*.^*.^!.^!.^!.^".^!.^!.^$.^2.^!.^!.^!.^".^".^!.^!.^".^2.^>.^>.^$.^>.^-.^0.^".	=:C;#FEEEEEEFEIEEECEEEEEGEHADLEIDFIEIDDEDDD?@DDEDDAGD>DEFEDBDADD#:JC?CCC?@=CCC==??CC?????C:?B?G#
Read 5 pileups for SRR1121656
1	NC_000001.10	249250621	linear
2	NC_000002.11	243199373	linear
3	NC_000003.11	198022430	linear
4	NC_000004.11	191154276	linear
5	NC_000005.9	180915260	linear
6	NC_000006.11	171115067	linear
7	NC_000007.13	159138663	linear
8	NC_000008.10	146364022	linear
9	NC_000009.11	141213431	linear
10	NC_000010.10	135534747	linear
11	NC_000011.9	135006516	linear
12	NC_000012.11	133851895	linear
13	NC_000013.10	115169878	linear
14	NC_000014.8	107349540	linear
15	NC_000015.9	102531392	linear
16	NC_000016.9	90354753	linear
17	NC_000017.10	81195210	linear
18	NC_000018.9	78077248	linear
19	NC_000019.9	59128983	linear
20	NC_000020.10	63025520	linear
21	NC_000021.8	48129895	linear
22	NC_000022.10	51304566	linear
X	NC_000023.10	155270560	linear
Y	NC_000024.9	59373566	linear
MT	NC_012920.1	16569	circular
GL000207.1	GL000207.1	4262	linear
GL000226.1	GL000226.1	15008	linear
GL000229.1	GL000229.1	19913	linear
GL000231.1	GL000231.1	27386	linear
GL000210.1	GL000210.1	27682	linear
GL000239.1	GL000239.1	33824	linear
GL000235.1	GL000235.1	34474	linear
GL000201.1	GL000201.1	36148	linear
GL000247.1	GL000247.1	36422	linear
GL000245.1	GL000245.1	36651	linear
GL000197.1	GL000197.1	37175	linear
GL000203.1	GL000203.1	37498	linear
GL000246.1	GL000246.1	38154	linear
GL000249.1	GL000249.1	38502	linear
GL000196.1	GL000196.1	38914	linear
GL000248.1	GL000248.1	39786	linear
GL000244.1	GL000244.1	39929	linear
GL000238.1	GL000238.1	39939	linear
GL000202.1	GL000202.1	40103	linear
GL000234.1	GL000234.1	40531	linear
GL000232.1	GL000232.1	40652	linear
GL000206.1	GL000206.1	41001	linear
GL000240.1	GL000240.1	41933	linear
GL000236.1	GL000236.1	41934	linear
GL000241.1	GL000241.1	42152	linear
GL000243.1	GL000243.1	43341	linear
GL000242.1	GL000242.1	43523	linear
GL000230.1	GL000230.1	43691	linear
GL000237.1	GL000237.1	45867	linear
GL000233.1	GL000233.1	45941	linear
GL000204.1	GL000204.1	81310	linear
GL000198.1	GL000198.1	90085	linear
GL000208.1	GL000208.1	92689	linear
GL000191.1	GL000191.1	106433	linear
GL000227.1	GL000227.1	128374	linear
GL000228.1	GL000228.1	129120	linear
GL000214.1	GL000214.1	137718	linear
GL000221.1	GL000221.1	155397	linear
GL000209.1	GL000209.1	159169	linear
GL000218.1	GL000218.1	161147	linear
GL000220.1	GL000220.1	161802	linear
GL000213.1	GL000213.1	164239	linear
GL000211.1	GL000211.1	166566	linear
GL000199.1	GL000199.1	169874	linear
GL000217.1	GL000217.1	172149	linear
GL000216.1	GL000216.1	172294	linear
GL000215.1	GL000215.1	172545	linear
GL000205.1	GL000205.1	174588	linear
GL000219.1	GL000219.1	179198	linear
GL000224.1	GL000224.1	179693	linear
GL000223.1	GL000223.1	180455	linear
GL000195.1	GL000195.1	182896	linear
GL000212.1	GL000212.1	186858	linear
GL000222.1	GL000222.1	186861	linear
GL000200.1	GL000200.1	187035	linear
GL000193.1	GL000193.1	189789	linear
GL000194.1	GL000194.1	191469	linear
GL000225.1	GL000225.1	211173	linear
GL000192.1	GL000192.1	547496	linear
NC_007605	NC_007605.1	171823	linear
hs37d5	hs37d5	35477943	linear
Read 0 references for SRR1121656