[ensembl-dev] HG883_PATCH
Amonida Zadissa
amonida at ebi.ac.uk
Tue Apr 1 11:13:42 BST 2014
Hi G,
Sorry for the delay in replying to your question.
The list of regions that you find in the gtf file and also in the
toplevel dump refer to several different assembly groups.
All the GL regions are scaffolds on the primary assembly. These are
regions that are either unplaced, that is, they are not linked to a
chromosome or, unlocalised meaning that it is known which chromosome
they map to but their chromosomal coordinates or their orientation is
not known. In Ensembl, these regions are called 'Supercontigs' in human.
There are 7 haplotypes on chromosome 6 corresponding to the MHC region:
HSCHR6_MHC_APD
HSCHR6_MHC_COX
HSCHR6_MHC_DBB
HSCHR6_MHC_MANN
HSCHR6_MHC_MCF
HSCHR6_MHC_QBL
HSCHR6_MHC_SSTO
Additionally, there are two more haplotypes, one on chromosome 4,
HSCHR4_1, and one on chromosome 17, HSCHR17_1.
Rest of the non-chromosomal regions are GRC patch regions, either a FIX
or a NOVEL patch. In addition to the GRC information that Kerstin sent,
you can find more details on how we represent assemblies in Ensembl, and
more specifically the human assembly on the page below:
http://www.ensembl.org/info/genome/genebuild/assembly.html
Hope this helps and again sorry for the late reply.
Cheers,
Amonida
On 31/03/2014 19:27, Kerstin Howe wrote:
> Hi Genomeo,
>
> I'm not an ensembl developer, but on the Genome Reference Consortium's
> web pages, you can find info on the patches at
> http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/patches.shtml,
> and all patches for GRCh37.p13 are listed in
> ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/PATCHES/alt_scaffolds/patch_type.
>
>
> Hope this helps,
>
> Kerstin
>
>
> On 31 Mar 2014, at 17:37, Genomeo Dev <genomeodev at gmail.com
> <mailto:genomeodev at gmail.com>> wrote:
>
>> Hi,
>>
>> Any response from the developers on the question about the patches please?
>>
>> Regards,
>>
>> G.
>>
>>
>> On 25 March 2014 14:43, Genomeo Dev <genomeodev at gmail.com
>> <mailto:genomeodev at gmail.com>> wrote:
>>
>> Hi,
>>
>> The gtf file:
>>
>> ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
>>
>> contains the below unique list of regions. What are these
>> categories of patches refer to? Are these all fix patches or also
>> novel ones? GL, HG_PATCH, HG_HG_PATCH, HG_HG_NOVEL_TEST, HSCHR,
>> HSCHR_CTG, HSCHR_MHC, HSCHR_LRC, HSCHR_HG.
>>
>> Thanks,
>>
>> Genomeo
>>
>> 1
>> 2
>> 3
>> 4
>> 5
>> 6
>> 7
>> 8
>> 9
>> 10
>> 11
>> 12
>> 13
>> 14
>> 15
>> 16
>> 17
>> 18
>> 19
>> 20
>> 21
>> 22
>> GL000191.1
>> GL000192.1
>> GL000193.1
>> GL000194.1
>> GL000195.1
>> GL000196.1
>> GL000199.1
>> GL000201.1
>> GL000204.1
>> GL000205.1
>> GL000209.1
>> GL000211.1
>> GL000212.1
>> GL000213.1
>> GL000215.1
>> GL000216.1
>> GL000218.1
>> GL000219.1
>> GL000220.1
>> GL000221.1
>> GL000222.1
>> GL000223.1
>> GL000224.1
>> GL000225.1
>> GL000228.1
>> GL000229.1
>> GL000230.1
>> GL000231.1
>> GL000233.1
>> GL000236.1
>> GL000237.1
>> GL000240.1
>> GL000241.1
>> GL000242.1
>> GL000243.1
>> GL000247.1
>> HG1007_PATCH
>> HG1032_PATCH
>> HG104_HG975_PATCH
>> HG1063_PATCH
>> HG1074_PATCH
>> HG1079_PATCH
>> HG1082_HG167_PATCH
>> HG1091_PATCH
>> HG1133_PATCH
>> HG1146_PATCH
>> HG115_PATCH
>> HG1208_PATCH
>> HG1211_PATCH
>> HG122_PATCH
>> HG1257_PATCH
>> HG1287_PATCH
>> HG1292_PATCH
>> HG1293_PATCH
>> HG1304_PATCH
>> HG1308_PATCH
>> HG1322_PATCH
>> HG1350_HG959_PATCH
>> HG1423_PATCH
>> HG1424_PATCH
>> HG1425_PATCH
>> HG1426_PATCH
>> HG142_HG150_NOVEL_TEST
>> HG1433_PATCH
>> HG1434_PATCH
>> HG1435_PATCH
>> HG1436_HG1432_PATCH
>> HG1437_PATCH
>> HG1438_PATCH
>> HG1439_PATCH
>> HG1440_PATCH
>> HG1441_PATCH
>> HG1442_PATCH
>> HG1443_HG1444_PATCH
>> HG144_PATCH
>> HG1453_PATCH
>> HG1458_PATCH
>> HG1459_PATCH
>> HG1462_PATCH
>> HG1463_PATCH
>> HG1472_PATCH
>> HG1479_PATCH
>> HG1486_PATCH
>> HG1487_PATCH
>> HG1488_PATCH
>> HG1490_PATCH
>> HG1497_PATCH
>> HG14_PATCH
>> HG1500_PATCH
>> HG1501_PATCH
>> HG1502_PATCH
>> HG151_NOVEL_TEST
>> HG1591_PATCH
>> HG1592_PATCH
>> HG1595_PATCH
>> HG1699_PATCH
>> HG174_HG254_PATCH
>> HG183_PATCH
>> HG185_PATCH
>> HG186_PATCH
>> HG193_PATCH
>> HG19_PATCH
>> HG237_PATCH
>> HG243_PATCH
>> HG256_PATCH
>> HG271_PATCH
>> HG27_PATCH
>> HG280_PATCH
>> HG281_PATCH
>> HG299_PATCH
>> HG29_PATCH
>> HG305_PATCH
>> HG306_PATCH
>> HG311_PATCH
>> HG325_PATCH
>> HG329_PATCH
>> HG339_PATCH
>> HG344_PATCH
>> HG348_PATCH
>> HG357_PATCH
>> HG375_PATCH
>> HG385_PATCH
>> HG388_HG400_PATCH
>> HG414_PATCH
>> HG417_PATCH
>> HG418_PATCH
>> HG444_PATCH
>> HG480_HG481_PATCH
>> HG497_PATCH
>> HG506_HG507_HG1000_PATCH
>> HG50_PATCH
>> HG531_PATCH
>> HG536_PATCH
>> HG544_PATCH
>> HG686_PATCH
>> HG706_PATCH
>> HG729_PATCH
>> HG730_PATCH
>> HG736_PATCH
>> HG745_PATCH
>> HG747_PATCH
>> HG748_PATCH
>> HG75_PATCH
>> HG79_PATCH
>> HG7_PATCH
>> HG858_PATCH
>> HG865_PATCH
>> HG871_PATCH
>> HG873_PATCH
>> HG883_PATCH
>> HG905_PATCH
>> HG944_PATCH
>> HG946_PATCH
>> HG953_PATCH
>> HG957_PATCH
>> HG962_PATCH
>> HG971_PATCH
>> HG979_PATCH
>> HG987_PATCH
>> HG989_PATCH
>> HG990_PATCH
>> HG991_PATCH
>> HG996_PATCH
>> HG998_1_PATCH
>> HG998_2_PATCH
>> HG999_1_PATCH
>> HG999_2_PATCH
>> HSCHR10_1_CTG2
>> HSCHR10_1_CTG5
>> HSCHR1_1_CTG31
>> HSCHR12_1_CTG1
>> HSCHR12_1_CTG2_1
>> HSCHR12_1_CTG5
>> HSCHR12_2_CTG2
>> HSCHR12_2_CTG2_1
>> HSCHR12_3_CTG2_1
>> HSCHR1_2_CTG31
>> HSCHR1_3_CTG31
>> HSCHR15_1_CTG4
>> HSCHR15_1_CTG8
>> HSCHR16_1_CTG3_1
>> HSCHR16_2_CTG3_1
>> HSCHR17_1
>> HSCHR17_1_CTG1
>> HSCHR17_1_CTG4
>> HSCHR17_2_CTG4
>> HSCHR17_3_CTG4
>> HSCHR17_4_CTG4
>> HSCHR17_5_CTG4
>> HSCHR17_6_CTG4
>> HSCHR18_1_CTG1_1
>> HSCHR18_1_CTG2_1
>> HSCHR18_2_CTG2
>> HSCHR18_2_CTG2_1
>> HSCHR19_1_CTG3
>> HSCHR19_1_CTG3_1
>> HSCHR19_2_CTG3
>> HSCHR19_3_CTG3
>> HSCHR19LRC_COX1_CTG1
>> HSCHR19LRC_COX2_CTG1
>> HSCHR19LRC_LRC_I_CTG1
>> HSCHR19LRC_LRC_J_CTG1
>> HSCHR19LRC_LRC_S_CTG1
>> HSCHR19LRC_LRC_T_CTG1
>> HSCHR19LRC_PGF1_CTG1
>> HSCHR19LRC_PGF2_CTG1
>> HSCHR20_1_CTG1
>> HSCHR21_2_CTG1_1
>> HSCHR21_3_CTG1_1
>> HSCHR21_4_CTG1_1
>> HSCHR2_1_CTG1
>> HSCHR2_1_CTG12
>> HSCHR22_1_CTG1
>> HSCHR22_1_CTG2
>> HSCHR22_2_CTG1
>> HSCHR2_2_CTG12
>> HSCHR3_1_CTG1
>> HSCHR3_1_CTG2_1
>> HSCHR4_1
>> HSCHR4_1_CTG12
>> HSCHR4_1_CTG6
>> HSCHR4_2_CTG9
>> HSCHR5_1_CTG1
>> HSCHR5_1_CTG2
>> HSCHR5_1_CTG5
>> HSCHR5_2_CTG1
>> HSCHR5_3_CTG1
>> HSCHR6_1_CTG5
>> HSCHR6_MHC_APD
>> HSCHR6_MHC_COX
>> HSCHR6_MHC_DBB
>> HSCHR6_MHC_MANN
>> HSCHR6_MHC_MCF
>> HSCHR6_MHC_QBL
>> HSCHR6_MHC_SSTO
>> HSCHR7_1_CTG6
>> HSCHR9_1_CTG1
>> HSCHR9_1_CTG35
>> HSCHR9_2_CTG35
>> HSCHR9_3_CTG35
>> MT
>> X
>> Y
>>
>>
>>
>> On 24 March 2014 07:58, mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>>
>> wrote:
>>
>> Hi Enrico,
>>
>> HG883_PATCH is indeed a patch.
>> The human reference assembly contains fix patches, which
>> attempt to correct sequencing errors in the primary assembly,
>> as well as novel patches, or haplotypes.
>> More information here:
>> http://www.ensembl.org/Help/__Glossary?id=297
>> <http://www.ensembl.org/Help/Glossary?id=297>
>>
>> HG883_PATCH is located on chromosome 17, as can be seen on
>> this view:
>> http://www.ensembl.org/Homo___sapiens/Location/View?db=core;__r=HG883_PATCH:26729129-__26731068
>> <http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=HG883_PATCH:26729129-26731068>
>> If you click outside of the green region, it will tell you
>> which chromosome you are on.
>>
>> LRGs are Locus Reference Genomic.
>> These provide an assembly-independent gene location and are
>> mainly used by the diagnostic community.
>> More information here:
>> http://www.ensembl.org/Help/__Glossary?id=406
>> <http://www.ensembl.org/Help/Glossary?id=406>
>>
>> To ensure the uniqueness of a sequence, you should align it
>> against the primary assembly, hence excluding all alternative
>> sequences.
>> On our ftp site
>> (ftp://ftp.ensembl.org/pub/__release-75/fasta/homo_sapiens/__dna
>> <ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna>), the
>> sequence is called
>> Homo_sapiens.GRCh37.75.dna_sm.__primary_assembly.fa
>>
>>
>> Hope that helps,
>> Magali
>>
>>
>> On 24/03/2014 05:33, Enrico Rubagotti wrote:
>>
>> Hi all,
>> I wish to ensure the uniqueness of ENST00000003834 in the
>> human genome.
>> To achieve this objective I blasted ENST00000003834
>> (identity value =100%) over the entire GRCh37.p13 and the
>> result was aligned to the Chr 17, and HG883_PATCH and LRG_183.
>> HG883_PATCH looks like a patch of the human genome, to
>> which chromosome it refers?
>> What is LRG_183?
>>
>> Please find below the result from blast
>>
>> Query=
>> ENSG00000004139|__ENST00000003834|26691378|__26728065|17
>> Length=2916
>> Score E
>> Sequences producing significant alignments: (Bits) Value
>>
>> ENSG00000004139|__ENST00000003834|26691378|__26728065|17
>> 5385 0.0
>> LRG_183|LRG_183t1|5001|16567|__LRG_183 3701 0.0
>> ENSG00000076351|__ENST00000583295|26721661|__26734215|17
>> 3701 0.0
>> ENSG00000076351|__ENST00000584729|26721661|__26734215|17
>> 3701 0.0
>> ENSG00000267556|__ENST00000591663|26691378|__26725182|HG883_PATCH
>> 1615 0.0
>> ENSG00000267556|__ENST00000585482|26691378|__26725182|HG883_PATCH
>> 1242 0.0
>> ENSG00000004139|__ENST00000578128|26691378|__26728065|17
>> 1242 0.0
>> ENSG00000004139|__ENST00000579593|26691378|__26728065|17
>> 1227 0.0
>> ENSG00000267556|__ENST00000585569|26691378|__26725182|HG883_PATCH
>> 660 0.0
>> ENSG00000004139|__ENST00000577870|26691378|__26728065|17
>> 660 0.0
>> ENSG00000267556|__ENST00000589014|26691378|__26725182|HG883_PATCH
>> 278 2e-72
>> ENSG00000004139|__ENST00000582323|26691378|__26728065|17
>> 278 2e-72
>> ENSG00000267556|__ENST00000591907|26691378|__26725182|HG883_PATCH
>> 154 3e-35
>>
>> Kind regards,
>>
>> Enrico
>>
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>>
>>
>> --
>> G.
>>
>>
>>
>>
>> --
>> G.
>> _______________________________________________
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>
> ---
> Dr. Kerstin Howe
> Senior Scientific Manager
> Genome Reference Informatics
> kerstin at sanger.ac.uk <mailto:kerstin at sanger.ac.uk>
>
> Wellcome Trust Sanger Institute
> Hinxton, Cambridge CB10 1SA, UK
>
>
>
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