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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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GRCh37 / hg19 / b37 / humanG1Kv37 - Human Reference Discrepancies
jonn
Member, Broadie, Moderator, Dev admin
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
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.
Source
The following are links to the GRCh37 reference:
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.
Source
The following are links to the hg19 reference:
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.
Source
The following are links to the b37 reference:
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 NC_007605). This reference grew out of the 1000 Genomes Project.
For details see the comparison table.
Source
The following are links to the HumanG1Kv37 reference:
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.
| MD5 | HumanG1Kv37 Contig | B37 Contig | HG19 Contig | GRCh37 Contig |
|---|---|---|---|---|
| 06cbf126247d89664a4faebad130fe9c | GL000202.1 | GL000202.1 | chr11_gl000202_random | GL000202.1 |
| 0996b4475f353ca98bacb756ac479140 | GL000244.1 | GL000244.1 | chrUn_gl000244 | GL000244.1 |
| 118a25ca210cfbcdfb6c2ebb249f9680 | GL000235.1 | GL000235.1 | chrUn_gl000235 | GL000235.1 |
| 131b1efc3270cc838686b54e7c34b17b | GL000238.1 | GL000238.1 | chrUn_gl000238 | GL000238.1 |
| 1c1b2cd1fccbc0a99b6a447fa24d1504 | GL000226.1 | GL000226.1 | chrUn_gl000226 | GL000226.1 |
| 1d708b54644c26c7e01c2dad5426d38c | GL000218.1 | GL000218.1 | chrUn_gl000218 | GL000218.1 |
| 1d78abec37c15fe29a275eb08d5af236 | GL000249.1 | GL000249.1 | chrUn_gl000249 | GL000249.1 |
| 2f8694fc47576bc81b5fe9e7de0ba49e | GL000242.1 | GL000242.1 | chrUn_gl000242 | GL000242.1 |
| 3238fb74ea87ae857f9c7508d315babb | GL000221.1 | GL000221.1 | chrUn_gl000221 | GL000221.1 |
| 325ba9e808f669dfeee210fdd7b470ac | GL000192.1 | GL000192.1 | chr1_gl000192_random | GL000192.1 |
| 399dfa03bf32022ab52a846f7ca35b30 | GL000223.1 | GL000223.1 | chrUn_gl000223 | GL000223.1 |
| 3e06b6741061ad93a8587531307057d8 | GL000232.1 | GL000232.1 | chrUn_gl000232 | GL000232.1 |
| 43f69e423533e948bfae5ce1d45bd3f1 | GL000206.1 | GL000206.1 | chr17_gl000206_random | GL000206.1 |
| 445a86173da9f237d7bcf41c6cb8cc62 | GL000240.1 | GL000240.1 | chrUn_gl000240 | GL000240.1 |
| 46c2032c37f2ed899eb41c0473319a69 | GL000214.1 | GL000214.1 | chrUn_gl000214 | GL000214.1 |
| 563531689f3dbd691331fd6c5730a88b | GL000212.1 | GL000212.1 | chrUn_gl000212 | GL000212.1 |
| 569af3b73522fab4b40995ae4944e78e | GL000199.1 | GL000199.1 | chr9_gl000199_random | GL000199.1 |
| 5a8e43bec9be36c7b49c84d585107776 | GL000248.1 | GL000248.1 | chrUn_gl000248 | GL000248.1 |
| 5d9ec007868d517e73543b005ba48535 | GL000195.1 | GL000195.1 | chr7_gl000195_random | GL000195.1 |
| 5eb3b418480ae67a997957c909375a73 | GL000215.1 | GL000215.1 | chrUn_gl000215 | GL000215.1 |
| 63945c3e6962f28ffd469719a747e73c | GL000225.1 | GL000225.1 | chrUn_gl000225 | GL000225.1 |
| 642a232d91c486ac339263820aef7fe0 | GL000216.1 | GL000216.1 | chrUn_gl000216 | GL000216.1 |
| 6ac8f815bf8e845bb3031b73f812c012 | GL000194.1 | GL000194.1 | chr4_gl000194_random | GL000194.1 |
| 6d243e18dea1945fb7f2517615b8f52e | GL000217.1 | GL000217.1 | chrUn_gl000217 | GL000217.1 |
| 6f5efdd36643a9b8c8ccad6f2f1edc7b | GL000197.1 | GL000197.1 | chr8_gl000197_random | GL000197.1 |
| 6fe9abac455169f50470f5a6b01d0f59 | GL000222.1 | GL000222.1 | chrUn_gl000222 | GL000222.1 |
| 75e4c8d17cd4addf3917d1703cacaf25 | GL000200.1 | GL000200.1 | chr9_gl000200_random | GL000200.1 |
| 7daaa45c66b288847b9b32b964e623d3 | GL000211.1 | GL000211.1 | chrUn_gl000211 | GL000211.1 |
| 7de00226bb7df1c57276ca6baabafd15 | GL000247.1 | GL000247.1 | chrUn_gl000247 | GL000247.1 |
| 7e0e2e580297b7764e31dbc80c2540dd | X | X | chrX | chrX |
| 7fed60298a8d62ff808b74b6ce820001 | GL000233.1 | GL000233.1 | chrUn_gl000233 | GL000233.1 |
| 851106a74238044126131ce2a8e5847c | GL000210.1 | GL000210.1 | chr21_gl000210_random | GL000210.1 |
| 868e7784040da90d900d2d1b667a1383 | GL000198.1 | GL000198.1 | chr9_gl000198_random | GL000198.1 |
| 89bc61960f37d94abf0df2d481ada0ec | GL000245.1 | GL000245.1 | chrUn_gl000245 | GL000245.1 |
| 93f998536b61a56fd0ff47322a911d4b | GL000234.1 | GL000234.1 | chrUn_gl000234 | GL000234.1 |
| 96358c325fe0e70bee73436e8bb14dbd | GL000203.1 | GL000203.1 | chr17_gl000203_random | GL000203.1 |
| 99795f15702caec4fa1c4e15f8a29c07 | GL000239.1 | GL000239.1 | chrUn_gl000239 | GL000239.1 |
| 9d424fdcc98866650b58f004080a992a | GL000213.1 | GL000213.1 | chrUn_gl000213 | GL000213.1 |
| a4aead23f8053f2655e468bcc6ecdceb | GL000227.1 | GL000227.1 | chrUn_gl000227 | GL000227.1 |
| aa81be49bf3fe63a79bdc6a6f279abf6 | GL000208.1 | GL000208.1 | chr19_gl000208_random | GL000208.1 |
| b4eb71ee878d3706246b7c1dbef69299 | GL000230.1 | GL000230.1 | chrUn_gl000230 | GL000230.1 |
| ba8882ce3a1efa2080e5d29b956568a4 | GL000231.1 | GL000231.1 | chrUn_gl000231 | GL000231.1 |
| c5a17c97e2c1a0b6a9cc5a6b064b714f | GL000228.1 | GL000228.1 | chrUn_gl000228 | GL000228.1 |
| cc34279a7e353136741c9fce79bc4396 | GL000243.1 | GL000243.1 | chrUn_gl000243 | GL000243.1 |
| d0f40ec87de311d8e715b52e4c7062e1 | GL000229.1 | GL000229.1 | chrUn_gl000229 | GL000229.1 |
| d22441398d99caf673e9afb9a1908ec5 | GL000205.1 | GL000205.1 | chr17_gl000205_random | GL000205.1 |
| d5b2fc04f6b41b212a4198a07f450e20 | GL000224.1 | GL000224.1 | chrUn_gl000224 | GL000224.1 |
| d75b436f50a8214ee9c2a51d30b2c2cc | GL000191.1 | GL000191.1 | chr1_gl000191_random | GL000191.1 |
| d92206d1bb4c3b4019c43c0875c06dc0 | GL000196.1 | GL000196.1 | chr8_gl000196_random | GL000196.1 |
| dbb6e8ece0b5de29da56601613007c2a | GL000193.1 | GL000193.1 | chr4_gl000193_random | GL000193.1 |
| dfb7e7ec60ffdcb85cb359ea28454ee9 | GL000201.1 | GL000201.1 | chr9_gl000201_random | GL000201.1 |
| e0c82e7751df73f4f6d0ed30cdc853c0 | GL000237.1 | GL000237.1 | chrUn_gl000237 | GL000237.1 |
| e4afcd31912af9d9c2546acf1cb23af2 | GL000246.1 | GL000246.1 | chrUn_gl000246 | GL000246.1 |
| ef4258cdc5a45c206cea8fc3e1d858cf | GL000241.1 | GL000241.1 | chrUn_gl000241 | GL000241.1 |
| efc49c871536fa8d79cb0a06fa739722 | GL000204.1 | GL000204.1 | chr17_gl000204_random | GL000204.1 |
| f3814841f1939d3ca19072d9e89f3fd7 | GL000207.1 | GL000207.1 | chr18_gl000207_random | GL000207.1 |
| f40598e2a5a6b26e84a3775e0d1e2c81 | GL000209.1 | GL000209.1 | chr19_gl000209_random | GL000209.1 |
| f977edd13bac459cb2ed4a5457dba1b3 | GL000219.1 | GL000219.1 | chrUn_gl000219 | GL000219.1 |
| fc35de963c57bf7648429e6454f1c9db | GL000220.1 | GL000220.1 | chrUn_gl000220 | GL000220.1 |
| fdcd739913efa1fdc64b6c0cd7016779 | GL000236.1 | GL000236.1 | chrUn_gl000236 | GL000236.1 |
| 1b22b98cdeb4a9304cb5d48026a85128 | 1 | 1 | chr1 | chr1 |
| a0d9851da00400dec1098a9255ac712e | 2 | 2 | chr2 | chr2 |
| 23dccd106897542ad87d2765d28a19a1 | 4 | 4 | chr4 | chr4 |
| 0740173db9ffd264d728f32784845cd7 | 5 | 5 | chr5 | chr5 |
| 1d3a93a248d92a729ee764823acbbc6b | 6 | 6 | chr6 | chr6 |
| 618366e953d6aaad97dbe4777c29375e | 7 | 7 | chr7 | chr7 |
| 96f514a9929e410c6651697bded59aec | 8 | 8 | chr8 | chr8 |
| 3e273117f15e0a400f01055d9f393768 | 9 | 9 | chr9 | chr9 |
| 988c28e000e84c26d552359af1ea2e1d | 10 | 10 | chr10 | chr10 |
| 98c59049a2df285c76ffb1c6db8f8b96 | 11 | 11 | chr11 | chr11 |
| 51851ac0e1a115847ad36449b0015864 | 12 | 12 | chr12 | chr12 |
| 283f8d7892baa81b510a015719ca7b0b | 13 | 13 | chr13 | chr13 |
| 98f3cae32b2a2e9524bc19813927542e | 14 | 14 | chr14 | chr14 |
| e5645a794a8238215b2cd77acb95a078 | 15 | 15 | chr15 | chr15 |
| fc9b1a7b42b97a864f56b348b06095e6 | 16 | 16 | chr16 | chr16 |
| 351f64d4f4f9ddd45b35336ad97aa6de | 17 | 17 | chr17 | chr17 |
| b15d4b2d29dde9d3e4f93d1d0f2cbc9c | 18 | 18 | chr18 | chr18 |
| 1aacd71f30db8e561810913e0b72636d | 19 | 19 | chr19 | chr19 |
| 0dec9660ec1efaaf33281c0d5ea2560f | 20 | 20 | chr20 | chr20 |
| 2979a6085bfe28e3ad6f552f361ed74d | 21 | 21 | chr21 | chr21 |
| a718acaa6135fdca8357d5bfe94211dd | 22 | 22 | chr22 | chr22 |
| 1fa3474750af0948bdf97d5a0ee52e51 | Y | Y | ---- | ---- |
| 6743bd63b3ff2b5b8985d8933c53290a | ---- | NC_007605 | ---- | ---- |
| c68f52674c9fb33aef52dcf399755519 | MT | MT | ---- | chrM |
| fdfd811849cc2fadebc929bb925902e5 | 3 | 3 | ---- | ---- |
| 094d037050cad692b57ea12c4fef790f | ---- | ---- | chr6_qbl_hap6 | GL000255.1 |
| 18c17e1641ef04873b15f40f6c8659a4 | ---- | ---- | chr6_cox_hap2 | GL000251.1 |
| 1e86411d73e6f00a10590f976be01623 | ---- | ---- | chrY | chrY |
| 2a3c677c426a10e137883ae1ffb8da3f | ---- | ---- | chr6_dbb_hap3 | GL000252.1 |
| 3b6d666200e72bcc036bf88a4d7e0749 | ---- | ---- | chr6_ssto_hap7 | GL000256.1 |
| 641e4338fa8d52a5b781bd2a2c08d3c3 | ---- | ---- | chr3 | chr3 |
| 9d51d4152174461cd6715c7ddc588dc8 | ---- | ---- | chr6_mann_hap4 | GL000253.1 |
| d2ed829b8a1628d16cbeee88e88e39eb | ---- | ---- | chrM | ---- |
| d89517b400226d3b56e753972a7cad67 | ---- | ---- | chr17_ctg5_hap1 | GL000258.1 |
| efed415dd8742349cb7aaca054675b9a | ---- | ---- | chr6_mcf_hap5 | GL000254.1 |
| fa24f81b680df26bcfb6d69b784fbe36 | ---- | ---- | chr4_ctg9_hap1 | GL000257.1 |
| fe71bc63420d666884f37a3ad79f3317 | ---- | ---- | chr6_apd_hap1 | GL000250.1 |
| 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.
Post edited by jonn on
Comments
Sure - I'll try to round up my sources.
As an addendum - while some teams at the Broad use a few different references, the ones we most commonly use are B37 and HG38 (not listed here).
The link to B37 above is now correct (and hosted from our Google bucket).