GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies
Dictionary | Created 2019-01-29 | Last updated 2019-01-31


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0 - Introduction

This page explains the discrepancies between the different "hg19" references.

There are 4 common "hg19" references, and they are NOT directly interchangeable:

  • hg19 (ucsc.hg19.fasta, MD5sum: a244d8a32473650b25c6e8e1654387d6)
  • b37 (Homo_sapiens_assembly19.fasta, MD5sum: 886ba1559393f75872c1cf459eb57f2d)
  • GRCh37 (GRCh37.p13.genome.fasta, MD5sum: c140882eb2ea89bc2edfe934d51b66cc)
  • humanG1Kv37 (human_g1k_v37.fasta, MD5sum: 0ce84c872fc0072a885926823dcd0338)

0.1 - Table of Contents

  1. 0.0 Introduction
    1. 0.1 Table of Contents
  2. hg19
  3. GRCh37
  4. b37
  5. HumanG1Kv37
  6. Reference Comparison Table
  7. Additional Information

GRCh37

The Genome Reference Consortium Human Build 37, GRCh37, (GRCh37.p13.genome.fasta, MD5sum: c140882eb2ea89bc2edfe934d51b66cc) is a Homo Sapiens genome reference file built by the Genome Reference Consortium. This is a baseline human genome reference and serves as the basis for the other three references in this comparison.

For more information on GRCh37, visit the official Genome Reference Consortium website.

hg19

The University of California at Santa Cruz (UCSC) has created a reference based on GRCh37. This reference is often referred to as hg19 (ucsc.hg19.fasta, MD5sum: a244d8a32473650b25c6e8e1654387d6).

This reference contains some alterations from the baseline reference from the Genome Reference Consortium. These alterations largely consist of contig name changes, however there are known sequence differences on some contigs as well.

For details see the comparison table.

b37

The Broad Institute created a human genome reference file based on GRCh37. This reference is often referred to as b37 (Homo_sapiens_assembly19.fasta, MD5sum: 886ba1559393f75872c1cf459eb57f2d).

When people at The Broad Institute's Genomics Platform refer to the hg19 reference, they are actually referring to b37.

This reference contains some alterations from the baseline reference from the Genome Reference Consortium. These alterations largely consist of contig name changes, however there are known sequence differences on some contigs as well.

Anecdotally the changes are for bases for which there was low confidence. Those low confidence bases were then masked out in the b37 reference to be the IUPAC symbol for any base. However, there does not seem to be a detailed comparison readily available.

For details see the comparison table.

HumanG1Kv37

The humanG1Kv37 (human_g1k_v37.fasta, MD5sum: 0ce84c872fc0072a885926823dcd0338) reference is equivalent to b37, with the exception that it does not contain the decoy sequence for human herpesvirus 4 type 1 (named _NC007605).

Reference Comparison Table

The specific differences between these four references are detailed in the following table.

The contigs with identical MD5sums are specified in each row. In the case that the MD5sum does not match between the references (indicating a sequence difference), the row will have a blank entry for that contig (----).

Primary contigs with differing MD5sums are highlighted in red. Alternate contigs with differing MD5sums are highlighted in orange.

MD5HumanG1Kv37 ContigB37 ContigHG19 ContigGRCh37 Contig
06cbf126247d89664a4faebad130fe9cGL000202.1GL000202.1chr11_gl000202_randomGL000202.1
0996b4475f353ca98bacb756ac479140GL000244.1GL000244.1chrUn_gl000244GL000244.1
118a25ca210cfbcdfb6c2ebb249f9680GL000235.1GL000235.1chrUn_gl000235GL000235.1
131b1efc3270cc838686b54e7c34b17bGL000238.1GL000238.1chrUn_gl000238GL000238.1
1c1b2cd1fccbc0a99b6a447fa24d1504GL000226.1GL000226.1chrUn_gl000226GL000226.1
1d708b54644c26c7e01c2dad5426d38cGL000218.1GL000218.1chrUn_gl000218GL000218.1
1d78abec37c15fe29a275eb08d5af236GL000249.1GL000249.1chrUn_gl000249GL000249.1
2f8694fc47576bc81b5fe9e7de0ba49eGL000242.1GL000242.1chrUn_gl000242GL000242.1
3238fb74ea87ae857f9c7508d315babbGL000221.1GL000221.1chrUn_gl000221GL000221.1
325ba9e808f669dfeee210fdd7b470acGL000192.1GL000192.1chr1_gl000192_randomGL000192.1
399dfa03bf32022ab52a846f7ca35b30GL000223.1GL000223.1chrUn_gl000223GL000223.1
3e06b6741061ad93a8587531307057d8GL000232.1GL000232.1chrUn_gl000232GL000232.1
43f69e423533e948bfae5ce1d45bd3f1GL000206.1GL000206.1chr17_gl000206_randomGL000206.1
445a86173da9f237d7bcf41c6cb8cc62GL000240.1GL000240.1chrUn_gl000240GL000240.1
46c2032c37f2ed899eb41c0473319a69GL000214.1GL000214.1chrUn_gl000214GL000214.1
563531689f3dbd691331fd6c5730a88bGL000212.1GL000212.1chrUn_gl000212GL000212.1
569af3b73522fab4b40995ae4944e78eGL000199.1GL000199.1chr9_gl000199_randomGL000199.1
5a8e43bec9be36c7b49c84d585107776GL000248.1GL000248.1chrUn_gl000248GL000248.1
5d9ec007868d517e73543b005ba48535GL000195.1GL000195.1chr7_gl000195_randomGL000195.1
5eb3b418480ae67a997957c909375a73GL000215.1GL000215.1chrUn_gl000215GL000215.1
63945c3e6962f28ffd469719a747e73cGL000225.1GL000225.1chrUn_gl000225GL000225.1
642a232d91c486ac339263820aef7fe0GL000216.1GL000216.1chrUn_gl000216GL000216.1
6ac8f815bf8e845bb3031b73f812c012GL000194.1GL000194.1chr4_gl000194_randomGL000194.1
6d243e18dea1945fb7f2517615b8f52eGL000217.1GL000217.1chrUn_gl000217GL000217.1
6f5efdd36643a9b8c8ccad6f2f1edc7bGL000197.1GL000197.1chr8_gl000197_randomGL000197.1
6fe9abac455169f50470f5a6b01d0f59GL000222.1GL000222.1chrUn_gl000222GL000222.1
75e4c8d17cd4addf3917d1703cacaf25GL000200.1GL000200.1chr9_gl000200_randomGL000200.1
7daaa45c66b288847b9b32b964e623d3GL000211.1GL000211.1chrUn_gl000211GL000211.1
7de00226bb7df1c57276ca6baabafd15GL000247.1GL000247.1chrUn_gl000247GL000247.1
7e0e2e580297b7764e31dbc80c2540ddXXchrXchrX
7fed60298a8d62ff808b74b6ce820001GL000233.1GL000233.1chrUn_gl000233GL000233.1
851106a74238044126131ce2a8e5847cGL000210.1GL000210.1chr21_gl000210_randomGL000210.1
868e7784040da90d900d2d1b667a1383GL000198.1GL000198.1chr9_gl000198_randomGL000198.1
89bc61960f37d94abf0df2d481ada0ecGL000245.1GL000245.1chrUn_gl000245GL000245.1
93f998536b61a56fd0ff47322a911d4bGL000234.1GL000234.1chrUn_gl000234GL000234.1
96358c325fe0e70bee73436e8bb14dbdGL000203.1GL000203.1chr17_gl000203_randomGL000203.1
99795f15702caec4fa1c4e15f8a29c07GL000239.1GL000239.1chrUn_gl000239GL000239.1
9d424fdcc98866650b58f004080a992aGL000213.1GL000213.1chrUn_gl000213GL000213.1
a4aead23f8053f2655e468bcc6ecdcebGL000227.1GL000227.1chrUn_gl000227GL000227.1
aa81be49bf3fe63a79bdc6a6f279abf6GL000208.1GL000208.1chr19_gl000208_randomGL000208.1
b4eb71ee878d3706246b7c1dbef69299GL000230.1GL000230.1chrUn_gl000230GL000230.1
ba8882ce3a1efa2080e5d29b956568a4GL000231.1GL000231.1chrUn_gl000231GL000231.1
c5a17c97e2c1a0b6a9cc5a6b064b714fGL000228.1GL000228.1chrUn_gl000228GL000228.1
cc34279a7e353136741c9fce79bc4396GL000243.1GL000243.1chrUn_gl000243GL000243.1
d0f40ec87de311d8e715b52e4c7062e1GL000229.1GL000229.1chrUn_gl000229GL000229.1
d22441398d99caf673e9afb9a1908ec5GL000205.1GL000205.1chr17_gl000205_randomGL000205.1
d5b2fc04f6b41b212a4198a07f450e20GL000224.1GL000224.1chrUn_gl000224GL000224.1
d75b436f50a8214ee9c2a51d30b2c2ccGL000191.1GL000191.1chr1_gl000191_randomGL000191.1
d92206d1bb4c3b4019c43c0875c06dc0GL000196.1GL000196.1chr8_gl000196_randomGL000196.1
dbb6e8ece0b5de29da56601613007c2aGL000193.1GL000193.1chr4_gl000193_randomGL000193.1
dfb7e7ec60ffdcb85cb359ea28454ee9GL000201.1GL000201.1chr9_gl000201_randomGL000201.1
e0c82e7751df73f4f6d0ed30cdc853c0GL000237.1GL000237.1chrUn_gl000237GL000237.1
e4afcd31912af9d9c2546acf1cb23af2GL000246.1GL000246.1chrUn_gl000246GL000246.1
ef4258cdc5a45c206cea8fc3e1d858cfGL000241.1GL000241.1chrUn_gl000241GL000241.1
efc49c871536fa8d79cb0a06fa739722GL000204.1GL000204.1chr17_gl000204_randomGL000204.1
f3814841f1939d3ca19072d9e89f3fd7GL000207.1GL000207.1chr18_gl000207_randomGL000207.1
f40598e2a5a6b26e84a3775e0d1e2c81GL000209.1GL000209.1chr19_gl000209_randomGL000209.1
f977edd13bac459cb2ed4a5457dba1b3GL000219.1GL000219.1chrUn_gl000219GL000219.1
fc35de963c57bf7648429e6454f1c9dbGL000220.1GL000220.1chrUn_gl000220GL000220.1
fdcd739913efa1fdc64b6c0cd7016779GL000236.1GL000236.1chrUn_gl000236GL000236.1
1b22b98cdeb4a9304cb5d48026a8512811chr1chr1
a0d9851da00400dec1098a9255ac712e22chr2chr2
23dccd106897542ad87d2765d28a19a144chr4chr4
0740173db9ffd264d728f32784845cd755chr5chr5
1d3a93a248d92a729ee764823acbbc6b66chr6chr6
618366e953d6aaad97dbe4777c29375e77chr7chr7
96f514a9929e410c6651697bded59aec88chr8chr8
3e273117f15e0a400f01055d9f39376899chr9chr9
988c28e000e84c26d552359af1ea2e1d1010chr10chr10
98c59049a2df285c76ffb1c6db8f8b961111chr11chr11
51851ac0e1a115847ad36449b00158641212chr12chr12
283f8d7892baa81b510a015719ca7b0b1313chr13chr13
98f3cae32b2a2e9524bc19813927542e1414chr14chr14
e5645a794a8238215b2cd77acb95a0781515chr15chr15
fc9b1a7b42b97a864f56b348b06095e61616chr16chr16
351f64d4f4f9ddd45b35336ad97aa6de1717chr17chr17
b15d4b2d29dde9d3e4f93d1d0f2cbc9c1818chr18chr18
1aacd71f30db8e561810913e0b72636d1919chr19chr19
0dec9660ec1efaaf33281c0d5ea2560f2020chr20chr20
2979a6085bfe28e3ad6f552f361ed74d2121chr21chr21
a718acaa6135fdca8357d5bfe94211dd2222chr22chr22
1fa3474750af0948bdf97d5a0ee52e51YY--------
6743bd63b3ff2b5b8985d8933c53290a----NC_007605--------
c68f52674c9fb33aef52dcf399755519MTMT----chrM
fdfd811849cc2fadebc929bb925902e533--------
094d037050cad692b57ea12c4fef790f--------chr6_qbl_hap6GL000255.1
18c17e1641ef04873b15f40f6c8659a4--------chr6_cox_hap2GL000251.1
1e86411d73e6f00a10590f976be01623--------chrYchrY
2a3c677c426a10e137883ae1ffb8da3f--------chr6_dbb_hap3GL000252.1
3b6d666200e72bcc036bf88a4d7e0749--------chr6_ssto_hap7GL000256.1
641e4338fa8d52a5b781bd2a2c08d3c3--------chr3chr3
9d51d4152174461cd6715c7ddc588dc8--------chr6_mann_hap4GL000253.1
d2ed829b8a1628d16cbeee88e88e39eb--------chrM----
d89517b400226d3b56e753972a7cad67--------chr17_ctg5_hap1GL000258.1
efed415dd8742349cb7aaca054675b9a--------chr6_mcf_hap5GL000254.1
fa24f81b680df26bcfb6d69b784fbe36--------chr4_ctg9_hap1GL000257.1
fe71bc63420d666884f37a3ad79f3317--------chr6_apd_hap1GL000250.1
0386df1d3476e6649f919195cc072fc7------------GL383574.1
03de7a950b56720768373120bbddf693------------GL383558.1
03f5fa89e52d0fe155d2e3968bf2eeb7------------GL339450.1
049056a72b5aee0b3f876ddf554f0208------------JH720447.1
063358c8e7f81361b959efab7b3f15cc------------GL383565.1
07f56906bd56829f146dc0bf4b158603------------GL383538.1
09ce2d45f1f973e347e22ad1e3cf06fb------------GL383568.1
09d4cb1070e1c521d6e86e7038824c1c------------GL383544.1
0aee7c3e4bcc4c942230508c7836069b------------GL582967.1
0bdfd2a40e1ceab32d71d6f1c9a6ca32------------JH636056.1
0c787911df2449cbba8609bebf897ecb------------GL383541.1
0d12851232bcd8250e6dd61e3e7fd6a2------------JH636054.1
0db85f8e0ff66a470b46801c9892e471------------JH806589.1
0de582e28ae8c127d978b43e12a4f499------------KE332500.1
0f0364ed52ebe7757feea96ce623239f------------GL383529.1
10b523cdfd4f3707276ec92f0f9cddfb------------JH159133.1
1135da7b213739cfb3bdf2741c0c8083------------KE332506.1
122be4e189778434d8845fd5fd2c9a6b------------GL949748.1
12406aad3f3da31bda9c21a1aa0e16b6------------GL383539.1
12a3180640a49f33c960eb12ca61a6c4------------GL383542.1
13a8dc0d93c1bf1ae397593eba841721------------JH806573.1
1452be48789c27311d94561610f6d5af------------JH159132.1
157eecba5817aa1781a7bc4a9b60f933------------JH720446.1
15a2182cf9d3a55a7809adadc0775e03------------JH636060.1
16197ace4bfafdc2354857b98fc2a794------------GL582971.1
1668b0eb03be297f66837b46b5b73ac7------------JH806600.2
16a9ef53c176dcd2cf029940cbc29382------------JH720452.1
18c01f6e62136005ce1b2f2f33173f02------------GL582974.1
18fd9605f12ec0982adcf9e908f53331------------GL383523.1
190b4d20cab29ddba5f2495a7117f7cf------------JH636055.1
1919a95f3ea48fde56ba925295086028------------GL383582.2
192dead6bc331a0dcbd1ba9d3d8a6f80------------JH806581.1
1b6fa375fdf382778e6645d822d12254------------GL339449.2
1d217e666c48ef7f2ec81946f4f4bfcc------------GL383521.1
1d2933992f087a832718c9de19d4ceab------------KE332499.1
20d5046bbd2a21729fdd64fa94bdd5a1------------GL949742.1
20da91baf79b2e14b605a8ebe1f3704e------------GL877872.1
2118ff7bca8f75acc4629ab88bae1c2e------------GL582968.1
23aea04f46682e2a2be1a5ff3934a9fe------------GL383540.1
24f6ccbfc261e62451042a9713be6280------------JH636059.1
2536c2286fdeb98404ac410dbf528a3e------------GL949745.1
260aca5e1ff29b6ed3d3cd9e438f4219------------JH636053.3
2948653361f974fbed3e26a4dfbf332c------------GL383528.1
2cfa9ec8f70be88f95411dac6efb24c1------------JH159141.2
2e0bec27cfa9b440c746be52187fab0b------------GL383560.1
2f4f58e3b3a95bed1132833156340778------------GL383555.1
2fc316247e162f76a01012bbd9b665e6------------JH806603.1
321b3324431ae40e90a4117ecc07e93c------------JH591185.1
32ceefe714becfd36f207c5bffca4ba7------------GL877871.1
3342f6c21fa2dc364925712e0d52ed2d------------JH159148.1
348782844074360bdc8b6416e16cc5d0------------GL383549.1
349e96f115f829409bd1087b5fb684ca------------GL383519.1
35889722e6212fc9499e06e630268101------------JH806588.1
369f03e72d44461eab4542c58f3b5dcc------------KE332501.1
384b5b32f0ea2cfd15ac268a2ce07909------------JH159146.1
3893d44dfad7ce35744b2bde1e43bbd3------------GL383576.1
38e72cd57edb75d967ac2613d61d297d------------GL383563.2
3b40b7fdb005a1ce00efaa3310148852------------KE332502.1
3c5f20fb0744b7658d37d4ed79a286d1------------GL383520.1
3dd30a7638c3a3c518fc15571546b1be------------GL877875.1
3e0825dd23c9fce74a88d863e33c42b7------------JH159149.1
40015159c7da8f06875bb558587e3f07------------GL383571.1
404580d8ad56ded0fb33642c8b99c28b------------GL383537.1
4112dee892050e18ad279b8ebdcc5d48------------GL383578.1
41cf432193561894813a30da6e682e5b------------KB021647.1
447fe0ff3103170150280c775095eebf------------JH806593.1
44d5da56e5ec6ae0b9ebd354e9b47cfa------------JH159150.3
474baa8f6c6684c55bbc2a10bfa84baf------------GL949747.1
4791ba11d768da2cc1346d37a558047a------------GL582972.1
485c442c93fe19514153702f0c84d952------------GL582966.2
4a3d54bda53308ca941d6d0e794b05cb------------GL383554.1
4ad67c3a4e85f8b2cd54a8ef2aab4426------------GL383557.1
4bc4f02a4fca2c9d70646455bee8066e------------JH806596.1
50fd52ddb8ad2b024fb8b83a5c90a642------------JH806577.1
5404455aab275489bc8e6c9fb3ead5cb------------GL383573.1
54abe159678a84e88ceb2d5271027628------------KB663609.1
5835d9de56b65cefb9406d104d64531e------------GL383536.1
5950c02594cedbdf0fea5e8335e7cf80------------JH591181.2
5b90c3ac4e5938b400fcc2c29f3017bc------------GL949744.1
5b9d9fb059071e552bba531b81bd3472------------KB663606.1
5c3a364520bf7ed46894abdce8f6e032------------GL877876.1
5eb6da458990f121fae13ff83a4bcbca------------JH806576.1
5f9dc3f86463d08a1383cca5f285b7ad------------GL383570.1
5fae03628eb9a445571bac107823b394------------KE332505.1
620913159e2fbd4e931ac120e3c584c9------------GL383526.1
659b65783878ace88f4c4b165f239363------------JH636052.4
675046e52613269a7c2e803525bb5a33------------JH720445.1
67f26a755ca4c6ca9a8f567d80d15fb9------------JH159131.1
68391fb8f16a37b63f607b76702de3b1------------GL383583.1
69490aa24b00717f2b11c095a5339516------------JH720454.3
6b604cf3e324680b72716e814d805944------------GL383530.1
6b862a953dfe724a1f48eaf12a3b948a------------JH806578.1
6c22616c927261b8e5fc90028c780f00------------JH720444.2
6cba57c0e509ab785d3869134979b668------------GL383548.1
6d728406957c5c7fb158dbdb7efef2b7------------GL383527.1
6d85d704338ba29941aca4d278c7eb4a------------KB663608.1
6fbc7007a5ff8aae8b28ca52dd6d5571------------GL383531.1
71a0d13c09c3e7ee64c7740e1425f20e------------JH591183.1
73b240dd73b8bddcab281e265c9d759a------------GL383559.2
73d39b5d51e6e2e8d9549bb85d7dae04------------JH806579.1
741179e4ee12c60fbcc6eba4a5c7695b------------JH806598.1
74cff045a9cd92b7f571a756f248d16a------------GL383524.1
7b556f03729e304a286c8d7ef0f0c10e------------GL383547.1
7b6d6d01c18e91fc07f727ade2450f46------------JH806580.1
7d007a35ff02e56325881c68bb17b565------------GL949752.1
7e0afbdc97540aa0b101228b7bd331fb------------JH806591.1
8213c58e2c1c22397f0ad9d0d901bbdf------------JH159135.2
856a46516332f58a35eeb4f84d17febc------------JH159142.2
883b29a1e5975e0f3139c183fbe2596d------------GL383581.1
8a92722deabdf885d1aebfa8881d5903------------GL949753.1
8ac2dc8046e4bd0d6d46e827ff05ecd1------------JH806575.1
8ac9fb9d942dba38bfd30f8d767f4bba------------JH159136.1
8b1d46e46d3083625eac92e9363773dd------------KB663607.2
8d13c3e7cbb2b7e1a3225c5a54fe8f44------------GL383569.1
8e1004755b0574b2f855130c943fbd8e------------KB663603.1
8e4f862d5b37504199902c6685b7fee5------------GL383533.1
8ede6eec21d781c22a9801f51433fcd6------------JH806584.1
8fc7aaa775b43df3d77c9782a140a981------------GL383572.1
902d62224f09e59cb9c6c44f71b5fca3------------GL383580.1
90ad438579d919fd20c42bb4f48de64b------------JH591184.1
9133580f75d0ffa745af12953d65a4db------------GL383550.1
93001afcfc8594885490513c4ffe243e------------GL582977.2
93a798f03267e553445c7456c6f7ee49------------JH159143.1
94409f94ca59e67f811cd36ab133a82c------------GL877873.1
955e16dfcdb2d28a334349dfa39f2ed4------------KB021645.1
976c3a7c4051dd9ce879833f4a764289------------JH806590.2
978987018f1a910273ebcc387e038de8------------GL383518.1
9bb3fbcd1fc9c35884e0987755c55667------------GL949741.1
9bed9883963242dd74b883218d5f17bf------------GL383532.1
9d197695e8a47d4c30c891a53a0fd588------------JH720451.1
9dcedb7219aa23057244ca9a446f01ac------------JH806592.1
9e1fc7ed55646756ce109b12b82ff192------------JH159147.1
a009cf3116a844d7b2d467e672931bc5------------GL383564.1
a0584071d5a8e88fda38d4cca38704cb------------KB663605.1
a0bce2b33eb96adcb750622527225e7d------------JH720443.2
a0f25165c6537c9861cc1231f710e99f------------GL383566.1
a1dab5e9bbedd3539ace29af1f9d6139------------JH806595.1
a260ca7327d292deefef4f5fc7346dc4------------GL383561.2
a2ecd2eb53eb1737423d5a637e4374a9------------JH636058.1
a3bf927c2422ea0a661640669efd1081------------GL383577.1
a4053747fc0cf1e03fa6ae9cd5f821d0------------KB021648.1
aa5b0a15acec3c6177db764bd103d8a0------------JH720453.1
ab73a8d586ef4fc44dd063730b6aef39------------GL582973.1
abb9297c8b9dfc3013d416c803ff486c------------JH806601.1
ac9c384b2fc322b684128f1baf75785e------------JH591182.1
adb23c033121d433739de02cfa00c9fb------------JH806582.2
adec63ae44a39d716808cfee03b7a870------------JH806599.1
afb0d13ed9fa7518989caa0ec55aeb96------------GL949750.1
b293c854ddcbc316cb1d449bca46fbb3------------JH159137.1
b8864877618b25fc14f80e8538f23b77------------GL949751.1
b96f5e6bc844e8392d4e442aa7557e15------------KE332495.1
ba6a3b1599661e674918200a8d1333d3------------JH806594.1
bc6f64b0c4c934c2cea52bbe98639c79------------JH806583.1
bc79d1abee7076ea672293e12bd7ccb9------------GL383517.1
bd742a610e4bbc28fc00aaf71dfdc15d------------KB021644.1
be51fd8c00d62c3efc077a8e882062a4------------JH806586.1
bed6a2667e8452a176e93e921e0c21f6------------GL383556.1
c27dc6fea378fecf178a44682257c25e------------GL383545.1
c28f12c6ee0dec4cc6995766a710960c------------GL383552.1
c6ff49147dedce02366d6ade10580611------------GL383534.2
c86ffa095c924372aa455e43e61c96e8------------JH159145.1
ca0e3270f27bbee944844e44ec76659d------------JH806602.1
caebc01e3f44f7b2a559179b0261b77e------------GL383535.1
cca1c60136ec678eeef374134cd07a90------------GL877877.2
cdab95f32513753b3c0add3014afad3b------------JH806587.1
d08cc284ad35f0bd1eafb443c23ad8bd------------JH159138.1
d0b63f9cef6c4d382e49636465eab851------------GL877870.2
d0caa7bf982cf1e6ca8c8b833f56a21c------------JH806597.1
d4e2cf05984db16a78c953b898f5a86e------------GL582969.1
d76e635e75bc038782fb3d0c195d33fb------------GL949746.1
d8ef242a7373ff5657c8311b92dabfde------------JH591186.1
d9015dd9a0916a98ed8ab99fd3cdd012------------GL383567.1
d96719c32333013a51c4d6d3261f984f------------GL383551.1
d97cf75e24ed1370388fedf523faa7ab------------KE332496.1
da648c938f1bb43b41d254bd9a015cfb------------JH159139.1
dada6dd12ec844a3a13f547f4946428e------------JH159140.1
dd0bc538e31f35af2073daec1f378147------------JH159144.1
dd784bb8074d6f5b949464ffea8c6901------------JH720449.1
dd8730d9d33765ff135fcfadb8810280------------GL383575.2
df3e809f9a87f792218db18db51f6ad4------------GL383522.1
e0da36f2d1d2c6092f13d5bee52537e0------------GL383516.1
e0e934bd79ff323b31f4c9b80fb80a5c------------JH159134.2
e11adfbb638e60f61d7e8ef6647f30f2------------JH720448.1
e2cd68e2099fbd7cee557d6a7910768f------------KB021646.2
e363729ea23dad7c6802e7b439b4f668------------KE332497.1
e5b96eb9510763261839281c198607dd------------GL582979.2
e5cd94b0e0668debf81b82f405597b28------------GL582970.1
e6c232469067e8cadfa852a2ea5513b7------------GL949749.1
e8c870267b2a5261edb9d51d0efd6469------------GL582975.1
ebf72aeb4d53f0fd56e2e72967751f8a------------GL383562.1
ed6bcd4459b3bc6b366ce00262952f57------------GL949743.1
ed6fb45e0a25c31903cbb0f78d9d487e------------GL383546.1
edf086bce359065367b105cae0abfeee------------GL383579.1
edf41bfaf2584364bb4c5a645d73d53c------------GL383553.2
f2bfb99f84f2dd2ea538fe69ee786a0d------------GL383525.1
f486a5a44493d2e6bf72bf95ae898e3c------------JH806574.2
f7ee47af8d462cd9aeb6d40de99acb36------------JH806585.1
fa5fa49d281fc855dd1076c4f51bd8dc------------KE332498.1
faa48b73103366d1da02065870a58bda------------GL383543.1
faae4c952e9c38254538e1853b786276------------GL582976.1
fc93038463f9660e139435537ef53a5c------------KB663604.1
fdeb8db11e8544a638179a592c051331------------JH636061.1
fef0bc815f4826ea408515d8ec74ca80------------JH636057.1
ff7c4316cb69a8d571bd7ef85c1a10e4------------JH720455.1

This table indicates that while most contigs contain the same data, there are several with sequence differences between the references. Among those are Chromosome 3, Chromosome Y, and the Mitochondrial Contig.

Anecdotally the changes are for bases for which there was low confidence, with those low confidence bases masked out to be the IUPAC symbol for any base. However, there does not seem to be a detailed comparison readily available (i.e. there's no proof that this is true).

Therefore, when doing comparisons across the four reference versions for each of these contigs, some care should be taken.

Additional Information

Some further details can be found on this DNAnexus wiki page as of 2019/01/30.

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