==============================================================================
This file is from:
http://hgdownloads.cse.ucsc.edu/goldenPath/hg38/hg38Patch2/README.txt
GRCh38.p2 data is from:
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.17_GRCh38.p2/
Files in this directory:
hg38Patch2.fa.gz - GRCh38.p2 fasta sequences
hg38Patch2.2bit - GRCh38.p2 sequences in 2bit format
hg38Patch2.agp - GRCh38.p2 AGP structure definitions
md5sum.txt - MD5 sums to verify downloads of these files
Patch release 2 is the second patch release for the GRCh38 assembly.
Patch release 2 includes all contents that were in patch release 1.
This is a minor release of GRCh38 that does not disrupt the coordinate
system in the reference sequence GRCh38.
==============================================================================
Definitions:
Genome Patch: a sequence contig/scaffold that corrects sequence
in a major release of the genome, or adds sequence to it.
FIX patch: A patch that corrects sequence or reduces an assembly gap
in a given major release. FIX patch sequences are meant to be
incorporated into the primary or existing alt-loci assembly units at
the next major release, and their accessions will then be
deprecated.
NOVEL patch: A patch that adds sequence to a major release. Typically,
NOVEL patch sequences are meant to be incorporated into the assembly
as new alternate loci at the next major release, and their
accessions will not be deprecated. UCSC term: "New haplotype sequence"
Total patch scaffolds in this patch release: 31
27 patch scaffolds of type FIX
4 patch scaffolds of type NOVEL
==============================================================================
GRCh38 reference NCBI Entrez GRC region sequence patch
location nucleotide record name name type
chr1:17157487-17460319 chr1_KN538361v1_fix REGION200 HG2095_PATCH fix-patch
chr1:26512383-26678582 chr1_KN196473v1_fix REGION189 HG2058_PATCH fix-patch
chr1:41250328-41436604 chr1_KN196472v1_fix FOXO6 HG986_PATCH fix-patch
chr1:112909422-113029606 chr1_KN196474v1_fix REGION190 HG2104_PATCH fix-patch
chr1:210220259-210677001 chr1_KN538360v1_fix REGION199 HG1832_PATCH fix-patch
chr2:233054663-233420161 chr2_KN538363v1_fix REGION201 HG2232_PATCH fix-patch
chr2:239696904-239905046 chr2_KN538362v1_fix REGION202 HG2233_PATCH fix-patch
chr3:44474647-44925818 chr3_KN196475v1_fix REGION192 HG2066_PATCH fix-patch
chr3:72325441-72740399 chr3_KN538364v1_fix RYBP HG126_PATCH fix-patch
chr3:91247723-91553319 chr3_KN196476v1_fix REGION191 HG2022_PATCH fix-patch
chr5:21098347-21230960 chr5_KN196477v1_alt REGION193 HSCHR5_7_CTG1 novel-patch
chr6:67533466-67796090 chr6_KN196478v1_fix REGION194 HG2128_PATCH fix-patch
chr9:133174055-133504070 chr9_KN196479v1_fix ABO HG2030_PATCH fix-patch
chr10:38918270-39338430 chr10_KN538367v1_fix REGION205 HG2244_HG2245_PATCH fix-patch
chr10:74797382-75073121 chr10_KN196480v1_fix REGION195 HG2191_PATCH fix-patch
chr10:124109957-124195365 chr10_KN538366v1_fix REGION204 HG2242_HG2243_PATCH fix-patch
chr10:131588434-131607480 chr10_KN538365v1_fix REGION203 HG2241_PATCH fix-patch
chr11:7779133-7972558 chr11_KN538368v1_alt OLFACTORY_REGION_2 HSCHR11_1_CTG1_2 novel-patch
chr11:118978401-119087276 chr11_KN196481v1_fix SLC37A4 HG2217_PATCH fix-patch
chr12:12031003-12572035 chr12_KN538369v1_fix REGION206 HG1362_PATCH fix-patch
chr12:17717409-17928910 chr12_KN196482v1_fix REGION196 HG23_PATCH fix-patch
chr12:122057735-122145576 chr12_KN538370v1_fix REGION207 HG2247_PATCH fix-patch
chr13:18171249-18358106 chr13_KN538372v1_fix BAGE5 HG2291_PATCH fix-patch
chr13:86269523-86292877 chr13_KN196483v1_fix REGION197 HG2216_PATCH fix-patch
chr13:100900735-101049613 chr13_KN538373v1_fix REGION208 HG2249_PATCH fix-patch
chr13:113936976-114147229 chr13_KN538371v1_fix REGION209 HG2288_HG2289_PATCH fix-patch
chr19:39740125-40095774 chr19_KN196484v1_fix FCGBP HG2021_PATCH fix-patch
chr22:42077656-42253758 chr22_KN196485v1_alt CYP2D6 HSCHR22_4_CTG1 novel-patch
chr22:42077656-42253758 chr22_KN196486v1_alt CYP2D6 HSCHR22_5_CTG1 novel-patch
chrY:56821510-56887902 chrY_KN196487v1_fix REGION198 HG2062_PATCH fix-patch
chr15_KI270905v1_alt:1-5161414 chr15_KN538374v1_fix REGION1A HG2139_PATCH fix-patch
==============================================================================
Name Last modified Size Description
Parent Directory -
md5sum.txt 2015-01-20 13:49 150
hg38Patch2.fa.gz 2015-01-20 13:26 3.8M
hg38Patch2.agp 2015-01-13 13:32 11K
hg38Patch2.2bit 2015-01-13 13:32 3.4M