This directory contains FASTA files which contain a modified version
of the Dec. 2013 (GRCh38/hg38) reference human genome assembly.
The chromosomal sequences were assembled by the International Human
Genome Project sequencing centers.  The assembly sequence was changed
to use IUPAC ambiguous nucleotide characters at each base covered by a
stringently filtered subset of single-base substitutions annotated by
dbSNP build 144.  For example, if the assembly has an 'A' at a position
where dbSNP has annotated an A/C/T substitution SNP, the 'A' is replaced
by 'H' in the FASTA file here.

dbSNP single-base substitutions were excluded from masking in the
following cases:
- UCSC tagged the dbSNP item with any of these exceptions (see also the
  exceptions field of the hg38.snp144 database table as well as the
  hg38.snp144ExceptionDesc table):
  - MultipleAlignments: dbSNP mapped item to multiple locations
  - ObservedMismatch: the reference allele does not appear in the item's
    observed alleles.
  - ObservedWrongFormat: the observed sequence has an unexpected format
- dbSNP item class is not "single".
- dbSNP item length is not exactly one base.
- dbSNP item weight is greater than 1.  (lower weight = higher confidence)
The remaining single-base substitutions were used to mask the genomic
sequence.

Files included in this directory:

chr*.subst.fa.gz - FASTA files with IUPAC characters for substitution SNPs

md5sum.txt - checksums of files in this directory

------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/hg38/bigZips. To download multiple files, use
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/snp144Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/snp144Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/snp144Mask/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/snp144Mask/chr1.subst.fa.gz' 
        -O chr1.subst.fa.gz

To uncompress the fa.gz files:
    gunzip <file>.fa.gz

      Name                                Last modified      Size  Description
Parent Directory - md5sum.txt 2015-09-09 13:45 20K chrY.subst.fa.gz 2015-09-09 11:59 8.4M chrX_KI270913v1_alt.subst.fa.gz 2015-09-09 11:59 89K chrX_KI270881v1_alt.subst.fa.gz 2015-09-09 11:59 46K chrX_KI270880v1_alt.subst.fa.gz 2015-09-09 11:59 91K chrX.subst.fa.gz 2015-09-09 11:59 52M chrUn_KI270748v1.subst.fa.gz 2015-09-09 11:59 28K chrUn_KI270745v1.subst.fa.gz 2015-09-09 11:59 13K chrUn_KI270744v1.subst.fa.gz 2015-09-09 11:58 54K chrUn_KI270743v1.subst.fa.gz 2015-09-09 11:58 67K chrUn_KI270742v1.subst.fa.gz 2015-09-09 11:58 69K chrUn_GL000226v1.subst.fa.gz 2015-09-09 11:58 2.6K chrUn_GL000224v1.subst.fa.gz 2015-09-09 11:58 50K chrUn_GL000220v1.subst.fa.gz 2015-09-09 11:58 54K chrUn_GL000219v1.subst.fa.gz 2015-09-09 11:58 59K chrUn_GL000218v1.subst.fa.gz 2015-09-09 11:58 56K chrUn_GL000216v2.subst.fa.gz 2015-09-09 11:58 44K chrUn_GL000214v1.subst.fa.gz 2015-09-09 11:58 43K chrUn_GL000213v1.subst.fa.gz 2015-09-09 11:58 53K chrUn_GL000195v1.subst.fa.gz 2015-09-09 11:58 66K chrM.subst.fa.gz 2015-09-09 11:58 6.5K chr9_KI270823v1_alt.subst.fa.gz 2015-09-09 11:58 149K chr9_KI270719v1_random.subst.fa.gz 2015-09-09 11:58 57K chr9_KI270718v1_random.subst.fa.gz 2015-09-09 11:58 13K chr9_GL383542v1_alt.subst.fa.gz 2015-09-09 11:58 20K chr9_GL383541v1_alt.subst.fa.gz 2015-09-09 11:58 58K chr9_GL383539v1_alt.subst.fa.gz 2015-09-09 11:58 53K chr9.subst.fa.gz 2015-09-09 11:58 43M chr8_KI270926v1_alt.subst.fa.gz 2015-09-09 11:58 74K chr8_KI270901v1_alt.subst.fa.gz 2015-09-09 11:58 45K chr8_KI270900v1_alt.subst.fa.gz 2015-09-09 11:58 99K chr8_KI270822v1_alt.subst.fa.gz 2015-09-09 11:58 220K chr8_KI270821v1_alt.subst.fa.gz 2015-09-09 11:58 326K chr8_KI270820v1_alt.subst.fa.gz 2015-09-09 11:58 12K chr8_KI270819v1_alt.subst.fa.gz 2015-09-09 11:58 47K chr8_KI270818v1_alt.subst.fa.gz 2015-09-09 11:58 48K chr8_KI270817v1_alt.subst.fa.gz 2015-09-09 11:58 51K chr8_KI270816v1_alt.subst.fa.gz 2015-09-09 11:58 103K chr8_KI270815v1_alt.subst.fa.gz 2015-09-09 11:58 42K chr8_KI270814v1_alt.subst.fa.gz 2015-09-09 11:58 44K chr8_KI270813v1_alt.subst.fa.gz 2015-09-09 11:58 92K chr8_KI270812v1_alt.subst.fa.gz 2015-09-09 11:58 89K chr8_KI270811v1_alt.subst.fa.gz 2015-09-09 11:58 94K chr8_KI270810v1_alt.subst.fa.gz 2015-09-09 11:58 123K chr8.subst.fa.gz 2015-09-09 11:58 52M chr7_KI270899v1_alt.subst.fa.gz 2015-09-09 11:58 64K chr7_KI270809v1_alt.subst.fa.gz 2015-09-09 11:58 71K chr7_KI270808v1_alt.subst.fa.gz 2015-09-09 11:58 88K chr7_KI270807v1_alt.subst.fa.gz 2015-09-09 11:58 38K chr7_KI270806v1_alt.subst.fa.gz 2015-09-09 11:58 54K chr7_KI270805v1_alt.subst.fa.gz 2015-09-09 11:58 64K chr7_KI270804v1_alt.subst.fa.gz 2015-09-09 11:58 53K chr7_KI270803v1_alt.subst.fa.gz 2015-09-09 11:58 382K chr7_GL383534v2_alt.subst.fa.gz 2015-09-09 11:58 41K chr7.subst.fa.gz 2015-09-09 11:58 56M chr6_KI270802v1_alt.subst.fa.gz 2015-09-09 11:58 25K chr6_KI270801v1_alt.subst.fa.gz 2015-09-09 11:58 307K chr6_KI270800v1_alt.subst.fa.gz 2015-09-09 11:58 57K chr6_KI270799v1_alt.subst.fa.gz 2015-09-09 11:58 49K chr6_KI270798v1_alt.subst.fa.gz 2015-09-09 11:58 92K chr6_KI270797v1_alt.subst.fa.gz 2015-09-09 11:58 64K chr6_KI270758v1_alt.subst.fa.gz 2015-09-09 11:58 26K chr6_KB021644v2_alt.subst.fa.gz 2015-09-09 11:58 54K chr6_GL383533v1_alt.subst.fa.gz 2015-09-09 11:58 42K chr6_GL000256v2_alt.subst.fa.gz 2015-09-09 11:58 1.4M chr6_GL000255v2_alt.subst.fa.gz 2015-09-09 11:58 1.4M chr6_GL000254v2_alt.subst.fa.gz 2015-09-09 11:58 1.2M chr6_GL000253v2_alt.subst.fa.gz 2015-09-09 11:58 1.3M chr6_GL000252v2_alt.subst.fa.gz 2015-09-09 11:58 1.4M chr6_GL000251v2_alt.subst.fa.gz 2015-09-09 11:58 1.5M chr6_GL000250v2_alt.subst.fa.gz 2015-09-09 11:58 803K chr6.subst.fa.gz 2015-09-09 11:58 60M chr5_KI270898v1_alt.subst.fa.gz 2015-09-09 11:58 43K chr5_KI270897v1_alt.subst.fa.gz 2015-09-09 11:58 354K chr5_KI270796v1_alt.subst.fa.gz 2015-09-09 11:58 56K chr5_KI270795v1_alt.subst.fa.gz 2015-09-09 11:58 44K chr5_KI270794v1_alt.subst.fa.gz 2015-09-09 11:58 54K chr5_KI270793v1_alt.subst.fa.gz 2015-09-09 11:58 40K chr5_KI270792v1_alt.subst.fa.gz 2015-09-09 11:58 62K chr5_KI270791v1_alt.subst.fa.gz 2015-09-09 11:58 61K chr5_GL949742v1_alt.subst.fa.gz 2015-09-09 11:58 77K chr5_GL383532v1_alt.subst.fa.gz 2015-09-09 11:58 28K chr5_GL383531v1_alt.subst.fa.gz 2015-09-09 11:58 57K chr5_GL383530v1_alt.subst.fa.gz 2015-09-09 11:58 34K chr5_GL339449v2_alt.subst.fa.gz 2015-09-09 11:58 497K chr5_GL000208v1_random.subst.fa.gz 2015-09-09 11:58 24K chr5.subst.fa.gz 2015-09-09 11:58 64M chr4_KI270925v1_alt.subst.fa.gz 2015-09-09 11:58 183K chr4_KI270896v1_alt.subst.fa.gz 2015-09-09 11:57 127K chr4_KI270790v1_alt.subst.fa.gz 2015-09-09 11:57 72K chr4_KI270789v1_alt.subst.fa.gz 2015-09-09 11:57 66K chr4_KI270788v1_alt.subst.fa.gz 2015-09-09 11:57 52K chr4_KI270787v1_alt.subst.fa.gz 2015-09-09 11:57 36K chr4_KI270786v1_alt.subst.fa.gz 2015-09-09 11:57 82K chr4_KI270785v1_alt.subst.fa.gz 2015-09-09 11:57 40K chr4_GL383528v1_alt.subst.fa.gz 2015-09-09 11:57 120K chr4_GL383527v1_alt.subst.fa.gz 2015-09-09 11:57 54K chr4_GL000257v2_alt.subst.fa.gz 2015-09-09 11:57 197K chr4_GL000008v2_random.subst.fa.gz 2015-09-09 11:57 81K chr4.subst.fa.gz 2015-09-09 11:57 68M chr3_KI270937v1_alt.subst.fa.gz 2015-09-09 11:57 50K chr3_KI270936v1_alt.subst.fa.gz 2015-09-09 11:57 50K chr3_KI270935v1_alt.subst.fa.gz 2015-09-09 11:57 61K chr3_KI270934v1_alt.subst.fa.gz 2015-09-09 11:57 50K chr3_KI270924v1_alt.subst.fa.gz 2015-09-09 11:57 50K chr3_KI270895v1_alt.subst.fa.gz 2015-09-09 11:57 50K chr3_KI270784v1_alt.subst.fa.gz 2015-09-09 11:57 60K chr3_KI270783v1_alt.subst.fa.gz 2015-09-09 11:57 38K chr3_KI270782v1_alt.subst.fa.gz 2015-09-09 11:57 54K chr3_KI270781v1_alt.subst.fa.gz 2015-09-09 11:57 39K chr3_KI270780v1_alt.subst.fa.gz 2015-09-09 11:57 71K chr3_KI270779v1_alt.subst.fa.gz 2015-09-09 11:57 62K chr3_KI270778v1_alt.subst.fa.gz 2015-09-09 11:57 80K chr3_KI270777v1_alt.subst.fa.gz 2015-09-09 11:57 58K chr3_JH636055v2_alt.subst.fa.gz 2015-09-09 11:57 59K chr3_GL383526v1_alt.subst.fa.gz 2015-09-09 11:57 62K chr3_GL000221v1_random.subst.fa.gz 2015-09-09 11:57 51K chr3.subst.fa.gz 2015-09-09 11:57 71M chr2_KI270894v1_alt.subst.fa.gz 2015-09-09 11:57 65K chr2_KI270893v1_alt.subst.fa.gz 2015-09-09 11:57 53K chr2_KI270776v1_alt.subst.fa.gz 2015-09-09 11:57 56K chr2_KI270775v1_alt.subst.fa.gz 2015-09-09 11:57 45K chr2_KI270774v1_alt.subst.fa.gz 2015-09-09 11:57 69K chr2_KI270773v1_alt.subst.fa.gz 2015-09-09 11:57 24K chr2_KI270772v1_alt.subst.fa.gz 2015-09-09 11:57 39K chr2_KI270771v1_alt.subst.fa.gz 2015-09-09 11:57 36K chr2_KI270770v1_alt.subst.fa.gz 2015-09-09 11:57 46K chr2_KI270769v1_alt.subst.fa.gz 2015-09-09 11:57 40K chr22_KI270928v1_alt.subst.fa.gz 2015-09-09 11:57 56K chr22_KI270879v1_alt.subst.fa.gz 2015-09-09 11:57 100K chr22_KI270878v1_alt.subst.fa.gz 2015-09-09 11:57 62K chr22_KI270877v1_alt.subst.fa.gz 2015-09-09 11:57 35K chr22_KI270876v1_alt.subst.fa.gz 2015-09-09 11:57 86K chr22_KI270875v1_alt.subst.fa.gz 2015-09-09 11:57 88K chr22_KI270733v1_random.subst.fa.gz 2015-09-09 11:57 57K chr22_KI270731v1_random.subst.fa.gz 2015-09-09 11:57 48K chr22_KB663609v1_alt.subst.fa.gz 2015-09-09 11:57 22K chr22_GL383583v2_alt.subst.fa.gz 2015-09-09 11:57 33K chr22_GL383582v2_alt.subst.fa.gz 2015-09-09 11:57 53K chr22.subst.fa.gz 2015-09-09 11:57 13M chr21_KI270874v1_alt.subst.fa.gz 2015-09-09 11:57 53K chr21_KI270873v1_alt.subst.fa.gz 2015-09-09 11:57 47K chr2_KI270768v1_alt.subst.fa.gz 2015-09-09 11:57 36K chr2_KI270767v1_alt.subst.fa.gz 2015-09-09 11:57 53K chr2_GL582966v2_alt.subst.fa.gz 2015-09-09 11:57 32K chr2_GL383522v1_alt.subst.fa.gz 2015-09-09 11:57 42K chr2_GL383521v1_alt.subst.fa.gz 2015-09-09 11:57 47K chr21_KI270872v1_alt.subst.fa.gz 2015-09-09 11:57 28K chr21_GL383581v2_alt.subst.fa.gz 2015-09-09 11:57 39K chr21_GL383580v2_alt.subst.fa.gz 2015-09-09 11:57 26K chr21_GL383579v2_alt.subst.fa.gz 2015-09-09 11:57 67K chr21_GL383578v2_alt.subst.fa.gz 2015-09-09 11:57 21K chr21.subst.fa.gz 2015-09-09 11:57 14M chr20_KI270871v1_alt.subst.fa.gz 2015-09-09 11:57 19K chr20_KI270870v1_alt.subst.fa.gz 2015-09-09 11:57 56K chr20_KI270869v1_alt.subst.fa.gz 2015-09-09 11:56 38K chr20_GL383577v2_alt.subst.fa.gz 2015-09-09 11:56 42K chr20.subst.fa.gz 2015-09-09 11:56 22M chr2.subst.fa.gz 2015-09-09 11:56 86M chr1_KI270892v1_alt.subst.fa.gz 2015-09-09 11:56 54K chr1_KI270766v1_alt.subst.fa.gz 2015-09-09 11:56 83K chr19_KI270938v1_alt.subst.fa.gz 2015-09-09 11:56 328K chr1_KI270765v1_alt.subst.fa.gz 2015-09-09 11:56 60K chr1_KI270763v1_alt.subst.fa.gz 2015-09-09 11:56 294K chr1_KI270762v1_alt.subst.fa.gz 2015-09-09 11:56 99K chr1_KI270761v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr1_KI270760v1_alt.subst.fa.gz 2015-09-09 11:56 36K chr1_KI270759v1_alt.subst.fa.gz 2015-09-09 11:56 139K chr1_KI270714v1_random.subst.fa.gz 2015-09-09 11:56 14K chr1_KI270712v1_random.subst.fa.gz 2015-09-09 11:56 55K chr1_KI270710v1_random.subst.fa.gz 2015-09-09 11:56 14K chr1_KI270708v1_random.subst.fa.gz 2015-09-09 11:56 41K chr1_KI270707v1_random.subst.fa.gz 2015-09-09 11:56 10K chr1_KI270706v1_random.subst.fa.gz 2015-09-09 11:56 68K chr1_GL383520v2_alt.subst.fa.gz 2015-09-09 11:56 124K chr1_GL383519v1_alt.subst.fa.gz 2015-09-09 11:56 37K chr1_GL383518v1_alt.subst.fa.gz 2015-09-09 11:56 59K chr19_KI270933v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270932v1_alt.subst.fa.gz 2015-09-09 11:56 62K chr19_KI270931v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270930v1_alt.subst.fa.gz 2015-09-09 11:56 59K chr19_KI270929v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr19_KI270923v1_alt.subst.fa.gz 2015-09-09 11:56 57K chr19_KI270922v1_alt.subst.fa.gz 2015-09-09 11:56 56K chr19_KI270921v1_alt.subst.fa.gz 2015-09-09 11:56 81K chr19_KI270920v1_alt.subst.fa.gz 2015-09-09 11:56 59K chr19_KI270919v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270918v1_alt.subst.fa.gz 2015-09-09 11:56 37K chr19_KI270917v1_alt.subst.fa.gz 2015-09-09 11:56 57K chr19_KI270916v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr19_KI270915v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270914v1_alt.subst.fa.gz 2015-09-09 11:56 59K chr19_KI270891v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270890v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr19_KI270889v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270888v1_alt.subst.fa.gz 2015-09-09 11:56 47K chr19_KI270887v1_alt.subst.fa.gz 2015-09-09 11:56 62K chr19_KI270886v1_alt.subst.fa.gz 2015-09-09 11:56 59K chr19_KI270885v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270884v1_alt.subst.fa.gz 2015-09-09 11:56 47K chr19_KI270883v1_alt.subst.fa.gz 2015-09-09 11:56 51K chr19_KI270882v1_alt.subst.fa.gz 2015-09-09 11:56 71K chr19_KI270868v1_alt.subst.fa.gz 2015-09-09 11:56 19K chr19_KI270867v1_alt.subst.fa.gz 2015-09-09 11:56 75K chr19_KI270866v1_alt.subst.fa.gz 2015-09-09 11:56 13K chr19_KI270865v1_alt.subst.fa.gz 2015-09-09 11:56 16K chr19_GL949753v2_alt.subst.fa.gz 2015-09-09 11:56 210K chr19_GL949752v1_alt.subst.fa.gz 2015-09-09 11:56 303K chr19_GL949751v2_alt.subst.fa.gz 2015-09-09 11:56 147K chr19_GL949750v2_alt.subst.fa.gz 2015-09-09 11:56 134K chr19_GL949749v2_alt.subst.fa.gz 2015-09-09 11:56 139K chr19_GL949748v2_alt.subst.fa.gz 2015-09-09 11:56 145K chr19_GL949747v2_alt.subst.fa.gz 2015-09-09 11:56 205K chr19_GL949746v1_alt.subst.fa.gz 2015-09-09 11:56 274K chr19_GL383576v1_alt.subst.fa.gz 2015-09-09 11:56 64K chr19_GL383575v2_alt.subst.fa.gz 2015-09-09 11:56 57K chr19_GL383574v1_alt.subst.fa.gz 2015-09-09 11:56 52K chr19_GL383573v1_alt.subst.fa.gz 2015-09-09 11:56 122K chr19_GL000209v2_alt.subst.fa.gz 2015-09-09 11:56 52K chr19.subst.fa.gz 2015-09-09 11:56 20M chr18_KI270912v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr18_KI270911v1_alt.subst.fa.gz 2015-09-09 11:56 48K chr18_KI270864v1_alt.subst.fa.gz 2015-09-09 11:56 36K chr18_KI270863v1_alt.subst.fa.gz 2015-09-09 11:56 55K chr18_GL383572v1_alt.subst.fa.gz 2015-09-09 11:56 49K chr18_GL383571v1_alt.subst.fa.gz 2015-09-09 11:56 49K chr18_GL383570v1_alt.subst.fa.gz 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chr17_GL383565v1_alt.subst.fa.gz 2015-09-09 11:56 73K chr17_GL383564v2_alt.subst.fa.gz 2015-09-09 11:56 42K chr17_GL383563v3_alt.subst.fa.gz 2015-09-09 11:56 109K chr17_GL000258v2_alt.subst.fa.gz 2015-09-09 11:56 572K chr17_GL000205v2_random.subst.fa.gz 2015-09-09 11:56 60K chr17.subst.fa.gz 2015-09-09 11:56 28M chr16_KI270856v1_alt.subst.fa.gz 2015-09-09 11:56 21K chr16_KI270855v1_alt.subst.fa.gz 2015-09-09 11:56 76K chr16_KI270854v1_alt.subst.fa.gz 2015-09-09 11:56 46K chr16_KI270853v1_alt.subst.fa.gz 2015-09-09 11:56 870K chr16_KI270728v1_random.subst.fa.gz 2015-09-09 11:56 482K chr16_GL383557v1_alt.subst.fa.gz 2015-09-09 11:56 29K chr16_GL383556v1_alt.subst.fa.gz 2015-09-09 11:56 63K chr16.subst.fa.gz 2015-09-09 11:56 29M chr15_KI270906v1_alt.subst.fa.gz 2015-09-09 11:56 61K chr15_KI270905v1_alt.subst.fa.gz 2015-09-09 11:56 1.6M chr15_KI270852v1_alt.subst.fa.gz 2015-09-09 11:55 158K chr15_KI270851v1_alt.subst.fa.gz 2015-09-09 11:55 85K chr15_KI270850v1_alt.subst.fa.gz 2015-09-09 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