S10 Table: Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse 
Data files described here represent variations detected in six horses 
from six different breeds.  
The acronyms used in the file names refer to the following horse breeds:

    CH: Native Mongolian Chakouyi Horse
    MM: Mangalarga Marchador Horse
   AMH: American Miniature Horse
   ARB: Arabian Horse
   PER: Percheron Horse
   TWH: Tennessee Walking Horse 



o VCF File
    The file allsample.vcf.gz contains raw SNPs and Indels detected in the study using GATK v4.1.1.0 HaplotypeCaller procedure.


o Tracks (To be viewed using UCSC custom tracks):

1. SNPs: The file allsample_SNPeff_gatk.vcf.gz contains annotated SNPs and INDELs and can be viewd in a genome browser such as UCSC genome browser.

To upload the annotated SNPs and Indels, paste the following URL into the custom tracks submission box and click submit:

track type=vcfTabix name="Annotated SNPs+Indels" bigDataUrl=https://data.cyverse.org/dav-anon/iplant/home/abri1st/SNPs/allsample_SNPeff_gatk.vcf.gz



2. CNV_track Files
  These files contain CNVs detected using Control-FREEC. Copy number gains are displayed in red, Copy number losses are displayed in blue and normal copy numbers are
  displayed in green.


To upload the Copy Number variants, paste the following URLs into the custom tracks submission box and click submit:

For MM, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/MM_CNV.bed

For TWH, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/TWH_CNV.bed

For ARB, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/ARB_CNV.bed

For PER, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/PER_CNV.bed

For AMH, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/AMH_CNV.bed

For CH, use

https://data.cyverse.org/dav-anon/iplant/home/abri1st/CH_CNV.bed


3. Structural Variants (SVs):
  The file "Inter+Intra chromosomal SVs.txt" contains the SVs 
  and can be easily viewd using a standard text editor such as Notepad++.
  The types of SVs are SV_INTER for interchromosomal or SV_INTRA for
  intrachromosomal translocations.

To upload the Inter and Intra chromosomal structural variants, paste the following URL into the custom tracks submission box and click submit:

https://de.cyverse.org/dl/d/84EB1CBD-3261-4532-93C6-7451E79210A9/Inter_Intra_chromosomal_SVs_tracks.txt

o Description of the SVs:

  The following are the values and interpretation 
  of the inter and intra chromosomal translocations given in the track:
 
  NORMAL_SENSE: Correct ends orientation using < mates_orientation > as reference
  REVERSE_SENSE: One of the ends has an incorrect orientation
  DELETION: Deletion (NORMAL_SENSE & mean insert size > +threshold*sigma)
  INSERTION: Insertion (NORMAL_SENSE & mean insert size < -threshold*sigma)
  INVERSION: Inversion (REVERSE_SENSE)
  INV_FRAGMT: Inversion of a genomic fragment, defined by balanced signatures (BAL)
  INS_FRAGMT: Insertion of a genomic fragment, defined by balanced signatures (BAL)
  INV_INS_FRAGMT: Inverted INS_FRAGMT (BAL)
  LARGE_DUPLI: Large duplication
    (mates orientation=FR/RF & reversed mate sense & mean insert size > 
     +threshold*sigma & UNBAL) or
    (mates_orientation=FF/RR & ends order=normal/inverted & mean insert size > 
     +threshold*sigma & UNBAL)
  DUPLICATION: Duplication, medium size
    (mates_orientation=FR/RF & reversed mates orientation & mean insert size < 
     -threshold*sigma )
  SMALL_DUPLI: Small duplication
    (mean insert size < -threshold*sigma & overlap between subgroups)
  INV_DUPLI: Inverted duplication
    (REVERSE_SENSE & mean insert size < -threshold*sigma & UNBAL)
  TRANSLOC: Translocation
  INV_TRANSLOC: Inverted translocation
  COAMPLICON: Co-amplicons, two different fragments repeated in the same strand
    sense (BAL), ex: A > B > , A > B > A > B > 
  INV_COAMPLICON: Inverted co-amplicons, two different fragments repeated in the
    opposite strand sense (BAL), ex: A > B < , A > B < A > B < 
  SINGLETON: Singleton (mean insert size < -threshold*sigma), for Illumina mate-pairs only
  UNDEFINED: Undefined inter/intra-chromosomal SV type





For inquiries, please contact: 

1. Mohammed Al Abri (maa288cornell.edu) 
2. Samantha Brooks (samantha.brooksufl.edu)