@HD	VN:1.0	SO:coordinate
@SQ	SN:1	LN:249250621	M5:1b22b98cdeb4a9304cb5d48026a85128	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:2	LN:243199373	M5:a0d9851da00400dec1098a9255ac712e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:3	LN:198022430	M5:fdfd811849cc2fadebc929bb925902e5	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:4	LN:191154276	M5:23dccd106897542ad87d2765d28a19a1	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:5	LN:180915260	M5:0740173db9ffd264d728f32784845cd7	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:6	LN:171115067	M5:1d3a93a248d92a729ee764823acbbc6b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:7	LN:159138663	M5:618366e953d6aaad97dbe4777c29375e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:8	LN:146364022	M5:96f514a9929e410c6651697bded59aec	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:9	LN:141213431	M5:3e273117f15e0a400f01055d9f393768	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:10	LN:135534747	M5:988c28e000e84c26d552359af1ea2e1d	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:11	LN:135006516	M5:98c59049a2df285c76ffb1c6db8f8b96	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:12	LN:133851895	M5:51851ac0e1a115847ad36449b0015864	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:13	LN:115169878	M5:283f8d7892baa81b510a015719ca7b0b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:14	LN:107349540	M5:98f3cae32b2a2e9524bc19813927542e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:15	LN:102531392	M5:e5645a794a8238215b2cd77acb95a078	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:16	LN:90354753	M5:fc9b1a7b42b97a864f56b348b06095e6	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:17	LN:81195210	M5:351f64d4f4f9ddd45b35336ad97aa6de	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:18	LN:78077248	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:19	LN:59128983	M5:1aacd71f30db8e561810913e0b72636d	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:20	LN:63025520	M5:0dec9660ec1efaaf33281c0d5ea2560f	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:21	LN:48129895	M5:2979a6085bfe28e3ad6f552f361ed74d	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:22	LN:51304566	M5:a718acaa6135fdca8357d5bfe94211dd	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:X	LN:155270560	M5:7e0e2e580297b7764e31dbc80c2540dd	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:Y	LN:59373566	M5:1fa3474750af0948bdf97d5a0ee52e51	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:MT	LN:16569	M5:c68f52674c9fb33aef52dcf399755519	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000207.1	LN:4262	M5:f3814841f1939d3ca19072d9e89f3fd7	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000226.1	LN:15008	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000229.1	LN:19913	M5:d0f40ec87de311d8e715b52e4c7062e1	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000231.1	LN:27386	M5:ba8882ce3a1efa2080e5d29b956568a4	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000210.1	LN:27682	M5:851106a74238044126131ce2a8e5847c	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000239.1	LN:33824	M5:99795f15702caec4fa1c4e15f8a29c07	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000235.1	LN:34474	M5:118a25ca210cfbcdfb6c2ebb249f9680	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000201.1	LN:36148	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000247.1	LN:36422	M5:7de00226bb7df1c57276ca6baabafd15	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000245.1	LN:36651	M5:89bc61960f37d94abf0df2d481ada0ec	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000197.1	LN:37175	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000203.1	LN:37498	M5:96358c325fe0e70bee73436e8bb14dbd	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000246.1	LN:38154	M5:e4afcd31912af9d9c2546acf1cb23af2	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000249.1	LN:38502	M5:1d78abec37c15fe29a275eb08d5af236	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000196.1	LN:38914	M5:d92206d1bb4c3b4019c43c0875c06dc0	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000248.1	LN:39786	M5:5a8e43bec9be36c7b49c84d585107776	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000244.1	LN:39929	M5:0996b4475f353ca98bacb756ac479140	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000238.1	LN:39939	M5:131b1efc3270cc838686b54e7c34b17b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000202.1	LN:40103	M5:06cbf126247d89664a4faebad130fe9c	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000234.1	LN:40531	M5:93f998536b61a56fd0ff47322a911d4b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000232.1	LN:40652	M5:3e06b6741061ad93a8587531307057d8	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000206.1	LN:41001	M5:43f69e423533e948bfae5ce1d45bd3f1	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000240.1	LN:41933	M5:445a86173da9f237d7bcf41c6cb8cc62	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000236.1	LN:41934	M5:fdcd739913efa1fdc64b6c0cd7016779	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000241.1	LN:42152	M5:ef4258cdc5a45c206cea8fc3e1d858cf	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000243.1	LN:43341	M5:cc34279a7e353136741c9fce79bc4396	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000242.1	LN:43523	M5:2f8694fc47576bc81b5fe9e7de0ba49e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000230.1	LN:43691	M5:b4eb71ee878d3706246b7c1dbef69299	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000237.1	LN:45867	M5:e0c82e7751df73f4f6d0ed30cdc853c0	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000233.1	LN:45941	M5:7fed60298a8d62ff808b74b6ce820001	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000204.1	LN:81310	M5:efc49c871536fa8d79cb0a06fa739722	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000198.1	LN:90085	M5:868e7784040da90d900d2d1b667a1383	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000208.1	LN:92689	M5:aa81be49bf3fe63a79bdc6a6f279abf6	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000191.1	LN:106433	M5:d75b436f50a8214ee9c2a51d30b2c2cc	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000227.1	LN:128374	M5:a4aead23f8053f2655e468bcc6ecdceb	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000228.1	LN:129120	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000214.1	LN:137718	M5:46c2032c37f2ed899eb41c0473319a69	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000221.1	LN:155397	M5:3238fb74ea87ae857f9c7508d315babb	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000209.1	LN:159169	M5:f40598e2a5a6b26e84a3775e0d1e2c81	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000218.1	LN:161147	M5:1d708b54644c26c7e01c2dad5426d38c	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000220.1	LN:161802	M5:fc35de963c57bf7648429e6454f1c9db	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000213.1	LN:164239	M5:9d424fdcc98866650b58f004080a992a	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000211.1	LN:166566	M5:7daaa45c66b288847b9b32b964e623d3	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000199.1	LN:169874	M5:569af3b73522fab4b40995ae4944e78e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000217.1	LN:172149	M5:6d243e18dea1945fb7f2517615b8f52e	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000216.1	LN:172294	M5:642a232d91c486ac339263820aef7fe0	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000215.1	LN:172545	M5:5eb3b418480ae67a997957c909375a73	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000205.1	LN:174588	M5:d22441398d99caf673e9afb9a1908ec5	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000219.1	LN:179198	M5:f977edd13bac459cb2ed4a5457dba1b3	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000224.1	LN:179693	M5:d5b2fc04f6b41b212a4198a07f450e20	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000223.1	LN:180455	M5:399dfa03bf32022ab52a846f7ca35b30	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000195.1	LN:182896	M5:5d9ec007868d517e73543b005ba48535	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000212.1	LN:186858	M5:563531689f3dbd691331fd6c5730a88b	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000222.1	LN:186861	M5:6fe9abac455169f50470f5a6b01d0f59	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000200.1	LN:187035	M5:75e4c8d17cd4addf3917d1703cacaf25	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000193.1	LN:189789	M5:dbb6e8ece0b5de29da56601613007c2a	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000194.1	LN:191469	M5:6ac8f815bf8e845bb3031b73f812c012	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000225.1	LN:211173	M5:63945c3e6962f28ffd469719a747e73c	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:GL000192.1	LN:547496	M5:325ba9e808f669dfeee210fdd7b470ac	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:NC_007605	LN:171823	M5:6743bd63b3ff2b5b8985d8933c53290a	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@SQ	SN:hs37d5	LN:35477943	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz        AS:NCBI37       SP:Human
@RG	ID:SRR081026	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081048	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081052	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081081	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081085	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081094	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081099	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081114	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081151	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081169	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081177	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081213	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081293	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081296	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081357	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081412	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081419	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081447	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081452	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085541	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085544	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085596	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085616	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085622	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085698	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085699	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085718	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085729	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085777	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085780	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085784	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085790	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085846	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085856	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085879	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085908	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085910	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085925	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085947	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085974	LB:Solexa-42316	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081279	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081305	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081354	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081368	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR081445	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086005	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086033	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086038	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086039	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086045	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086054	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086071	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086076	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086116	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086120	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR086137	LB:Solexa-44770	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098564	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098579	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098580	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098588	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098593	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098618	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098652	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR098675	LB:Catch-36556	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR078977	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR078983	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR078985	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR078990	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR078994	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR079022	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR079040	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR079061	LB:Solexa-42057	SM:NA20766	PI:0	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085539	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085585	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085594	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085603	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085615	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085720	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085907	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@RG	ID:SRR085939	LB:Solexa-42057	SM:NA20766	PI:110	CN:BI	PL:ILLUMINA	DS:SRP004073
@PG	ID:bwa_index	PN:bwa	VN:0.5.9-r16	CL:bwa index -a bwtsw $reference_fasta
@PG	ID:bwa_aln_fastq	PN:bwa	PP:bwa_index	VN:0.5.9-r16	CL:bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file
@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa samse -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
@PG	ID:bwa_sam.1	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 330 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
@PG	ID:sam_to_fixed_bam	PN:samtools	PP:bwa_sam	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
@PG	ID:sam_to_fixed_bam.1	PN:samtools	PP:bwa_sam.1	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
@PG	ID:gatk_target_interval_creator	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
@PG	ID:gatk_target_interval_creator.1	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
@PG	ID:bam_realignment_around_known_indels	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
@PG	ID:bam_realignment_around_known_indels.1	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
@PG	ID:bam_count_covariates	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
@PG	ID:bam_count_covariates.1	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
@PG	ID:bam_recalibrate_quality_scores	PN:GenomeAnalysisTK	PP:bam_count_covariates	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
@PG	ID:bam_recalibrate_quality_scores.1	PN:GenomeAnalysisTK	PP:bam_count_covariates.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
@PG	ID:bam_calculate_bq	PN:samtools	PP:bam_recalibrate_quality_scores	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
@PG	ID:bam_calculate_bq.1	PN:samtools	PP:bam_recalibrate_quality_scores.1	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
@PG	ID:bam_merge	PN:picard	PP:bam_calculate_bq	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@PG	ID:bam_merge.1	PN:picard	PP:bam_calculate_bq.1	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@PG	ID:bam_mark_duplicates	PN:picard	PP:bam_merge	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
@PG	ID:bam_mark_duplicates.1	PN:picard	PP:bam_merge.1	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
@PG	ID:bam_merge.2	PN:picard	PP:bam_mark_duplicates	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@PG	ID:bam_merge.1.2	PN:picard	PP:bam_mark_duplicates.1	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
@CO	$known_indels_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.indels.sites.vcf.gz
@CO	$known_indels_file(s) .= ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.low_coverage_vqsr.20101123.indels.sites.vcf.gz
@CO	$known_sites_file(s) = ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_mapping_resources/ALL.wgs.dbsnp.build135.snps.sites.vcf.gz
SRR081094.764970	147	11	2798840	70	2S2M1I63M	=	2798746	-158	AACGGGGAGCAGCGGAATGGCTGTGCCCCCAGCCTGGAGTCAGGCCTGTGTCGCCCTGGGAGTGGAAT	###HFFGEGBA><EGCADDHDDF?ABCHFGDG<GCHGEHAGEHIHHCHBGBAIBCCBGGGCEAFE?=8	X0:i:1	X1:i:0	OC:Z:2S66M	XC:i:66	RG:Z:SRR081094	AM:i:37	NM:i:3	SM:i:37	OP:i:2798839	MQ:i:60	XT:A:U	BQ:Z:@@Bg@ca@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MD:Z:0A0C63
