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 150.  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.snp150 database table as well as the
  hg38.snp150ExceptionDesc 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

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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.soe.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.soe.ucsc.edu/goldenPath/hg38/snp150Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/hg38/snp150Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/snp150Mask/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/snp150Mask/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 - chr1.subst.fa.gz 2017-04-19 11:37 90M chr10.subst.fa.gz 2017-04-19 11:37 52M chr10_GL383545v1_alt.subst.fa.gz 2017-04-19 11:37 65K chr10_GL383546v1_alt.subst.fa.gz 2017-04-19 11:37 124K chr10_KI270824v1_alt.subst.fa.gz 2017-04-19 11:37 74K chr10_KI270825v1_alt.subst.fa.gz 2017-04-19 11:37 76K chr11.subst.fa.gz 2017-04-19 11:37 52M chr11_GL383547v1_alt.subst.fa.gz 2017-04-19 11:37 64K chr11_JH159136v1_alt.subst.fa.gz 2017-04-19 11:37 82K chr11_JH159137v1_alt.subst.fa.gz 2017-04-19 11:37 78K chr11_KI270826v1_alt.subst.fa.gz 2017-04-19 11:37 77K chr11_KI270827v1_alt.subst.fa.gz 2017-04-19 11:37 27K chr11_KI270829v1_alt.subst.fa.gz 2017-04-19 11:37 84K chr11_KI270830v1_alt.subst.fa.gz 2017-04-19 11:37 72K chr11_KI270831v1_alt.subst.fa.gz 2017-04-19 11:37 122K chr11_KI270832v1_alt.subst.fa.gz 2017-04-19 11:37 87K chr11_KI270902v1_alt.subst.fa.gz 2017-04-19 11:37 43K chr11_KI270903v1_alt.subst.fa.gz 2017-04-19 11:37 87K chr11_KI270927v1_alt.subst.fa.gz 2017-04-19 11:37 87K chr12.subst.fa.gz 2017-04-19 11:37 52M chr12_GL383549v1_alt.subst.fa.gz 2017-04-19 11:37 48K chr12_GL383550v2_alt.subst.fa.gz 2017-04-19 11:37 68K chr12_GL383551v1_alt.subst.fa.gz 2017-04-19 11:37 74K chr12_GL383552v1_alt.subst.fa.gz 2017-04-19 11:37 56K chr12_GL383553v2_alt.subst.fa.gz 2017-04-19 11:37 62K chr12_GL877875v1_alt.subst.fa.gz 2017-04-19 11:37 64K chr12_GL877876v1_alt.subst.fa.gz 2017-04-19 11:37 164K chr12_KI270833v1_alt.subst.fa.gz 2017-04-19 11:37 30K chr12_KI270834v1_alt.subst.fa.gz 2017-04-19 11:37 50K chr12_KI270835v1_alt.subst.fa.gz 2017-04-19 11:37 89K chr12_KI270836v1_alt.subst.fa.gz 2017-04-19 11:37 19K chr12_KI270837v1_alt.subst.fa.gz 2017-04-19 11:38 17K chr12_KI270904v1_alt.subst.fa.gz 2017-04-19 11:38 228K chr13.subst.fa.gz 2017-04-19 11:38 38M chr13_KI270838v1_alt.subst.fa.gz 2017-04-19 11:38 121K chr13_KI270839v1_alt.subst.fa.gz 2017-04-19 11:38 73K chr13_KI270840v1_alt.subst.fa.gz 2017-04-19 11:38 78K chr13_KI270841v1_alt.subst.fa.gz 2017-04-19 11:38 69K chr13_KI270842v1_alt.subst.fa.gz 2017-04-19 11:38 14K chr13_KI270843v1_alt.subst.fa.gz 2017-04-19 11:38 43K chr14.subst.fa.gz 2017-04-19 11:38 35M chr14_GL000009v2_random.subst.fa.gz 2017-04-19 11:38 80K chr14_GL000194v1_random.subst.fa.gz 2017-04-19 11:38 67K chr14_GL000225v1_random.subst.fa.gz 2017-04-19 11:38 58K chr14_KI270722v1_random.subst.fa.gz 2017-04-19 11:38 61K chr14_KI270723v1_random.subst.fa.gz 2017-04-19 11:38 13K chr14_KI270724v1_random.subst.fa.gz 2017-04-19 11:38 13K chr14_KI270725v1_random.subst.fa.gz 2017-04-19 11:38 57K chr14_KI270726v1_random.subst.fa.gz 2017-04-19 11:38 15K chr14_KI270844v1_alt.subst.fa.gz 2017-04-19 11:38 129K chr14_KI270845v1_alt.subst.fa.gz 2017-04-19 11:38 73K chr14_KI270846v1_alt.subst.fa.gz 2017-04-19 11:38 523K chr14_KI270847v1_alt.subst.fa.gz 2017-04-19 11:38 612K chr15.subst.fa.gz 2017-04-19 11:38 33M chr15_GL383554v1_alt.subst.fa.gz 2017-04-19 11:38 97K chr15_GL383555v2_alt.subst.fa.gz 2017-04-19 11:38 158K chr15_KI270727v1_random.subst.fa.gz 2017-04-19 11:38 146K chr15_KI270848v1_alt.subst.fa.gz 2017-04-19 11:38 126K chr15_KI270849v1_alt.subst.fa.gz 2017-04-19 11:38 96K chr15_KI270850v1_alt.subst.fa.gz 2017-04-19 11:38 155K chr15_KI270851v1_alt.subst.fa.gz 2017-04-19 11:38 94K chr15_KI270852v1_alt.subst.fa.gz 2017-04-19 11:38 161K chr15_KI270905v1_alt.subst.fa.gz 2017-04-19 11:39 1.8M chr15_KI270906v1_alt.subst.fa.gz 2017-04-19 11:39 72K chr16.subst.fa.gz 2017-04-19 11:39 32M chr16_GL383556v1_alt.subst.fa.gz 2017-04-19 11:39 75K chr16_GL383557v1_alt.subst.fa.gz 2017-04-19 11:39 36K chr16_KI270728v1_random.subst.fa.gz 2017-04-19 11:39 483K chr16_KI270853v1_alt.subst.fa.gz 2017-04-19 11:39 1.0M chr16_KI270854v1_alt.subst.fa.gz 2017-04-19 11:39 53K chr16_KI270855v1_alt.subst.fa.gz 2017-04-19 11:39 97K chr16_KI270856v1_alt.subst.fa.gz 2017-04-19 11:39 26K chr17.subst.fa.gz 2017-04-19 11:39 31M chr17_GL000205v2_random.subst.fa.gz 2017-04-19 11:39 61K chr17_GL000258v2_alt.subst.fa.gz 2017-04-19 11:39 648K chr17_GL383563v3_alt.subst.fa.gz 2017-04-19 11:39 132K chr17_GL383564v2_alt.subst.fa.gz 2017-04-19 11:39 55K chr17_GL383565v1_alt.subst.fa.gz 2017-04-19 11:39 91K chr17_GL383566v1_alt.subst.fa.gz 2017-04-19 11:39 32K chr17_JH159146v1_alt.subst.fa.gz 2017-04-19 11:39 110K chr17_JH159147v1_alt.subst.fa.gz 2017-04-19 11:39 29K chr17_JH159148v1_alt.subst.fa.gz 2017-04-19 11:39 36K chr17_KI270729v1_random.subst.fa.gz 2017-04-19 11:39 64K chr17_KI270730v1_random.subst.fa.gz 2017-04-19 11:39 24K chr17_KI270857v1_alt.subst.fa.gz 2017-04-19 11:39 1.1M chr17_KI270858v1_alt.subst.fa.gz 2017-04-19 11:39 98K chr17_KI270859v1_alt.subst.fa.gz 2017-04-19 11:39 45K chr17_KI270860v1_alt.subst.fa.gz 2017-04-19 11:39 72K chr17_KI270861v1_alt.subst.fa.gz 2017-04-19 11:39 81K chr17_KI270862v1_alt.subst.fa.gz 2017-04-19 11:39 155K chr17_KI270907v1_alt.subst.fa.gz 2017-04-19 11:39 55K chr17_KI270908v1_alt.subst.fa.gz 2017-04-19 11:39 547K chr17_KI270909v1_alt.subst.fa.gz 2017-04-19 11:39 114K chr17_KI270910v1_alt.subst.fa.gz 2017-04-19 11:39 63K chr18.subst.fa.gz 2017-04-19 11:39 30M chr18_GL383567v1_alt.subst.fa.gz 2017-04-19 11:39 116K chr18_GL383568v1_alt.subst.fa.gz 2017-04-19 11:39 43K chr18_GL383569v1_alt.subst.fa.gz 2017-04-19 11:39 65K chr18_GL383570v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr18_GL383571v1_alt.subst.fa.gz 2017-04-19 11:39 60K chr18_GL383572v1_alt.subst.fa.gz 2017-04-19 11:39 58K chr18_KI270863v1_alt.subst.fa.gz 2017-04-19 11:39 65K chr18_KI270864v1_alt.subst.fa.gz 2017-04-19 11:39 46K chr18_KI270911v1_alt.subst.fa.gz 2017-04-19 11:39 58K chr18_KI270912v1_alt.subst.fa.gz 2017-04-19 11:39 69K chr19.subst.fa.gz 2017-04-19 11:39 22M chr19_GL000209v2_alt.subst.fa.gz 2017-04-19 11:39 62K chr19_GL383573v1_alt.subst.fa.gz 2017-04-19 11:39 153K chr19_GL383574v1_alt.subst.fa.gz 2017-04-19 11:39 63K chr19_GL383575v2_alt.subst.fa.gz 2017-04-19 11:39 67K chr19_GL383576v1_alt.subst.fa.gz 2017-04-19 11:39 73K chr19_GL949746v1_alt.subst.fa.gz 2017-04-19 11:39 359K chr19_GL949747v2_alt.subst.fa.gz 2017-04-19 11:39 263K chr19_GL949748v2_alt.subst.fa.gz 2017-04-19 11:39 186K chr19_GL949749v2_alt.subst.fa.gz 2017-04-19 11:39 179K chr19_GL949750v2_alt.subst.fa.gz 2017-04-19 11:39 174K chr19_GL949751v2_alt.subst.fa.gz 2017-04-19 11:39 189K chr19_GL949752v1_alt.subst.fa.gz 2017-04-19 11:39 395K chr19_GL949753v2_alt.subst.fa.gz 2017-04-19 11:39 274K chr19_KI270865v1_alt.subst.fa.gz 2017-04-19 11:39 22K chr19_KI270866v1_alt.subst.fa.gz 2017-04-19 11:39 18K chr19_KI270867v1_alt.subst.fa.gz 2017-04-19 11:39 90K chr19_KI270868v1_alt.subst.fa.gz 2017-04-19 11:39 26K chr19_KI270882v1_alt.subst.fa.gz 2017-04-19 11:39 92K chr19_KI270883v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270884v1_alt.subst.fa.gz 2017-04-19 11:39 61K chr19_KI270885v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270886v1_alt.subst.fa.gz 2017-04-19 11:39 77K chr19_KI270887v1_alt.subst.fa.gz 2017-04-19 11:39 81K chr19_KI270888v1_alt.subst.fa.gz 2017-04-19 11:39 61K chr19_KI270889v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270890v1_alt.subst.fa.gz 2017-04-19 11:39 69K chr19_KI270891v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270914v1_alt.subst.fa.gz 2017-04-19 11:39 76K chr19_KI270915v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270916v1_alt.subst.fa.gz 2017-04-19 11:39 69K chr19_KI270917v1_alt.subst.fa.gz 2017-04-19 11:39 76K chr19_KI270918v1_alt.subst.fa.gz 2017-04-19 11:39 49K chr19_KI270919v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270920v1_alt.subst.fa.gz 2017-04-19 11:39 79K chr19_KI270921v1_alt.subst.fa.gz 2017-04-19 11:39 92K chr1_GL383518v1_alt.subst.fa.gz 2017-04-19 11:39 71K chr1_GL383519v1_alt.subst.fa.gz 2017-04-19 11:39 43K chr1_GL383520v2_alt.subst.fa.gz 2017-04-19 11:39 143K chr1_KI270706v1_random.subst.fa.gz 2017-04-19 11:39 73K chr1_KI270707v1_random.subst.fa.gz 2017-04-19 11:39 10K chr19_KI270922v1_alt.subst.fa.gz 2017-04-19 11:39 75K chr19_KI270923v1_alt.subst.fa.gz 2017-04-19 11:39 74K chr19_KI270929v1_alt.subst.fa.gz 2017-04-19 11:39 74K chr19_KI270930v1_alt.subst.fa.gz 2017-04-19 11:39 77K chr19_KI270931v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270932v1_alt.subst.fa.gz 2017-04-19 11:39 79K chr19_KI270933v1_alt.subst.fa.gz 2017-04-19 11:39 68K chr19_KI270938v1_alt.subst.fa.gz 2017-04-19 11:39 434K chr1_KI270708v1_random.subst.fa.gz 2017-04-19 11:39 42K chr1_KI270709v1_random.subst.fa.gz 2017-04-19 11:39 19K chr1_KI270710v1_random.subst.fa.gz 2017-04-19 11:39 15K chr1_KI270711v1_random.subst.fa.gz 2017-04-19 11:39 14K chr1_KI270712v1_random.subst.fa.gz 2017-04-19 11:39 55K chr1_KI270713v1_random.subst.fa.gz 2017-04-19 11:39 14K chr1_KI270714v1_random.subst.fa.gz 2017-04-19 11:39 15K chr1_KI270759v1_alt.subst.fa.gz 2017-04-19 11:39 144K chr1_KI270760v1_alt.subst.fa.gz 2017-04-19 11:39 45K chr1_KI270761v1_alt.subst.fa.gz 2017-04-19 11:39 63K chr1_KI270762v1_alt.subst.fa.gz 2017-04-19 11:39 109K chr1_KI270763v1_alt.subst.fa.gz 2017-04-19 11:39 364K chr1_KI270764v1_alt.subst.fa.gz 2017-04-19 11:39 21K chr1_KI270765v1_alt.subst.fa.gz 2017-04-19 11:39 61K chr1_KI270766v1_alt.subst.fa.gz 2017-04-19 11:40 91K chr1_KI270892v1_alt.subst.fa.gz 2017-04-19 11:40 63K chr2.subst.fa.gz 2017-04-19 11:40 95M chr20.subst.fa.gz 2017-04-19 11:40 24M chr20_GL383577v2_alt.subst.fa.gz 2017-04-19 11:40 51K chr20_KI270869v1_alt.subst.fa.gz 2017-04-19 11:40 48K chr20_KI270870v1_alt.subst.fa.gz 2017-04-19 11:40 70K chr20_KI270871v1_alt.subst.fa.gz 2017-04-19 11:40 23K chr21.subst.fa.gz 2017-04-19 11:40 15M chr21_GL383578v2_alt.subst.fa.gz 2017-04-19 11:40 26K chr21_GL383579v2_alt.subst.fa.gz 2017-04-19 11:40 80K chr21_GL383580v2_alt.subst.fa.gz 2017-04-19 11:40 31K chr21_GL383581v2_alt.subst.fa.gz 2017-04-19 11:40 46K chr21_KI270872v1_alt.subst.fa.gz 2017-04-19 11:40 34K chr2_GL383521v1_alt.subst.fa.gz 2017-04-19 11:41 61K chr2_GL383522v1_alt.subst.fa.gz 2017-04-19 11:41 50K chr2_GL582966v2_alt.subst.fa.gz 2017-04-19 11:41 39K chr21_KI270873v1_alt.subst.fa.gz 2017-04-19 11:41 58K chr21_KI270874v1_alt.subst.fa.gz 2017-04-19 11:41 64K chr22.subst.fa.gz 2017-04-19 11:41 15M chr22_GL383582v2_alt.subst.fa.gz 2017-04-19 11:41 68K chr22_GL383583v2_alt.subst.fa.gz 2017-04-19 11:41 37K chr22_KB663609v1_alt.subst.fa.gz 2017-04-19 11:41 28K chr22_KI270731v1_random.subst.fa.gz 2017-04-19 11:41 48K chr22_KI270732v1_random.subst.fa.gz 2017-04-19 11:41 14K chr22_KI270733v1_random.subst.fa.gz 2017-04-19 11:41 57K chr22_KI270734v1_random.subst.fa.gz 2017-04-19 11:41 53K chr22_KI270735v1_random.subst.fa.gz 2017-04-19 11:41 14K chr22_KI270736v1_random.subst.fa.gz 2017-04-19 11:41 42K chr22_KI270737v1_random.subst.fa.gz 2017-04-19 11:41 25K chr22_KI270738v1_random.subst.fa.gz 2017-04-19 11:41 25K chr22_KI270739v1_random.subst.fa.gz 2017-04-19 11:41 16K chr22_KI270875v1_alt.subst.fa.gz 2017-04-19 11:41 105K chr22_KI270876v1_alt.subst.fa.gz 2017-04-19 11:41 106K chr22_KI270877v1_alt.subst.fa.gz 2017-04-19 11:41 42K chr22_KI270878v1_alt.subst.fa.gz 2017-04-19 11:41 72K chr22_KI270879v1_alt.subst.fa.gz 2017-04-19 11:41 118K chr22_KI270928v1_alt.subst.fa.gz 2017-04-19 11:41 73K chr2_KI270715v1_random.subst.fa.gz 2017-04-19 11:41 17K chr2_KI270716v1_random.subst.fa.gz 2017-04-19 11:41 19K chr2_KI270767v1_alt.subst.fa.gz 2017-04-19 11:41 58K chr2_KI270768v1_alt.subst.fa.gz 2017-04-19 11:41 43K chr2_KI270769v1_alt.subst.fa.gz 2017-04-19 11:41 49K chr2_KI270770v1_alt.subst.fa.gz 2017-04-19 11:41 53K chr2_KI270771v1_alt.subst.fa.gz 2017-04-19 11:41 46K chr2_KI270772v1_alt.subst.fa.gz 2017-04-19 11:41 48K chr2_KI270773v1_alt.subst.fa.gz 2017-04-19 11:41 29K chr2_KI270774v1_alt.subst.fa.gz 2017-04-19 11:41 88K chr2_KI270775v1_alt.subst.fa.gz 2017-04-19 11:41 57K chr2_KI270776v1_alt.subst.fa.gz 2017-04-19 11:41 69K chr2_KI270893v1_alt.subst.fa.gz 2017-04-19 11:41 58K chr2_KI270894v1_alt.subst.fa.gz 2017-04-19 11:41 76K chr3.subst.fa.gz 2017-04-19 11:41 78M chr3_GL000221v1_random.subst.fa.gz 2017-04-19 11:41 51K chr3_GL383526v1_alt.subst.fa.gz 2017-04-19 11:41 70K chr3_JH636055v2_alt.subst.fa.gz 2017-04-19 11:41 69K chr3_KI270777v1_alt.subst.fa.gz 2017-04-19 11:41 71K chr3_KI270778v1_alt.subst.fa.gz 2017-04-19 11:41 101K chr3_KI270779v1_alt.subst.fa.gz 2017-04-19 11:41 71K chr3_KI270780v1_alt.subst.fa.gz 2017-04-19 11:41 90K chr3_KI270781v1_alt.subst.fa.gz 2017-04-19 11:41 43K chr3_KI270782v1_alt.subst.fa.gz 2017-04-19 11:41 63K chr3_KI270783v1_alt.subst.fa.gz 2017-04-19 11:41 45K chr3_KI270784v1_alt.subst.fa.gz 2017-04-19 11:41 68K chr3_KI270895v1_alt.subst.fa.gz 2017-04-19 11:41 64K chr3_KI270924v1_alt.subst.fa.gz 2017-04-19 11:41 65K chr3_KI270934v1_alt.subst.fa.gz 2017-04-19 11:41 64K chr3_KI270935v1_alt.subst.fa.gz 2017-04-19 11:41 78K chr3_KI270936v1_alt.subst.fa.gz 2017-04-19 11:42 65K chr3_KI270937v1_alt.subst.fa.gz 2017-04-19 11:42 65K chr4.subst.fa.gz 2017-04-19 11:42 75M chr4_GL000008v2_random.subst.fa.gz 2017-04-19 11:42 84K chr4_GL000257v2_alt.subst.fa.gz 2017-04-19 11:42 238K chr4_GL383527v1_alt.subst.fa.gz 2017-04-19 11:42 66K chr4_GL383528v1_alt.subst.fa.gz 2017-04-19 11:42 143K chr4_KI270785v1_alt.subst.fa.gz 2017-04-19 11:42 48K chr4_KI270786v1_alt.subst.fa.gz 2017-04-19 11:42 94K chr4_KI270787v1_alt.subst.fa.gz 2017-04-19 11:42 46K chr4_KI270788v1_alt.subst.fa.gz 2017-04-19 11:42 64K chr4_KI270789v1_alt.subst.fa.gz 2017-04-19 11:42 80K chr4_KI270790v1_alt.subst.fa.gz 2017-04-19 11:42 90K chr4_KI270896v1_alt.subst.fa.gz 2017-04-19 11:42 146K chr4_KI270925v1_alt.subst.fa.gz 2017-04-19 11:42 215K chr5.subst.fa.gz 2017-04-19 11:42 71M chr5_GL000208v1_random.subst.fa.gz 2017-04-19 11:42 24K chr5_GL339449v2_alt.subst.fa.gz 2017-04-19 11:42 532K chr5_GL383530v1_alt.subst.fa.gz 2017-04-19 11:42 35K chr5_GL383531v1_alt.subst.fa.gz 2017-04-19 11:42 70K chr5_GL383532v1_alt.subst.fa.gz 2017-04-19 11:42 33K chr5_GL949742v1_alt.subst.fa.gz 2017-04-19 11:42 85K chr5_KI270791v1_alt.subst.fa.gz 2017-04-19 11:42 80K chr5_KI270792v1_alt.subst.fa.gz 2017-04-19 11:42 70K 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