Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse – University of Copenhagen

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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Alignments to the horse genome reference EquCab2.0

Files available through Prof. Ludovic Orlando:

Modern horses

- Arabian  11.03X (15 GB); index (.bai)

- Icelandic 8.43X (12 GB); index (.bai)

- Norwegian Fjord 7.86X (12 GB); index (.bai)

- Przewalski 9.61X (14 GB); index (.bai)

- Standardbred 12.16X (17 GB); index (.bai)

- Twilight (Thoroughbred) 21.08X (38 GB); index (.bai)

Ancient horses

- Middle Pleistocene horse from Thistle Creek, 560-780 Ky BP, 1.12X

  • illumina data 0.74X (1.7 GB); index (.bai)
  • helicos data 0.38X (1 GB); index (.bai)

- Late Pleistocene horse from Taymyr peninsula, CGG10022, 43 Ky BP 1.78X (4.3 GB); index (.bai)

Modern domestic donkey

- Willy 12.40X (29 GB); index (.bai)

Alignments to the donkey de novo assembly, BAM files

Modern horses

- Arabian 9.3X (13 GB); index (.bai)

- Icelandic 7.0X (9.8 GB); index (.bai)

- Norwegian Fjord 6.7X (9.6 GB); index (.bai)

- Przewalski 8.2X (12 GB); index (.bai)

- Standardbred 10.4X (14 GB); index (.bai)

- Twilight (Thoroughbred) 18.5X (35 GB); index (.bai)

Ancient horses

- Middle Pleistocene horse from Thistle Creek, 560-780 Ky BP, 0.98X

  • illumina data 0.63X (1.4 GB); index (.bai)
  • helicos data 0.35X (920 MB); index (.bai)

- Late Pleistocene horse from Taymyr peninsula, CGG10022, 43 Ky BP 0.79X (2.0 GB); index (.bai)

Modern domestic donkey

- Willy 12.0X, (26 GB); index (.bai)

Sequences of donkey de novo assembly scaffolds, FASTA file

- Willy (gzipped) 666 MB

SNPs to the horse genome reference EquCab2.0, VCF files

Modern horses

- Arabian (bzip2ed) 43 MB

- Icelandic (bzip2ed) 38 MB

- Norwegian Fjord (bzip2ed) 37 MB

- Przewalski (bzip2ed) 48 MB

- Standardbred (bzip2ed) 49 MB

- Twilight (Thoroughbred, bzip2ed) 43 MB

Modern domestic donkey

- Willy (bzip2ed) 246 MB

SNPs to the donkey de novo assembly, VCF files

Modern horses

- Arabian (bzip2ed) 152 MB

- Icelandic (bzip2ed) 113 MB

- Norwegian Fjord (bzip2ed) 114 MB

- Przewalski (bzip2ed) 143 MB

- Standardbred (bzip2ed) 171 MB

- Twilight (Thoroughbred, bzip2ed) 254 MB

Modern domestic donkey

- Willy (bzip2ed) 38 MB

Proteomics data

Middle Pleistocene horse from Thistle Creek, sample TC21.1

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S48, MSM file

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S48, raw file

 

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S51, MSM file

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S51, raw file

 

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S53, MSM file

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S53, raw file

 

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S56, MSM file

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S56, raw file

 

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S58, MSM file

- 20110419_Velos1_JVO_COLLAB_Enrico-KyoHorse_S58, raw file

Middle Pleistocene horse from Thistle Creek, sample TC21.2

- 20111024_QE4_QC_COLLAB_083HORSE2FR2POSTTRYP01, MSM file

- 20111024_QE4_QC_COLLAB_083HORSE2FR2POSTTRYP01, raw file

 

- 20111024_QE4_QC_COLLAB_084HORSE2PTPOSTTRYP01, MSM file

- 20111024_QE4_QC_COLLAB_084HORSE2PTPOSTTRYP01, raw file

 

- 20111024_QE4_QC_COLLAB_091HORSE2FR101, MSM file

- 20111024_QE4_QC_COLLAB_091HORSE2FR101, raw file

 

- 20111024_QE4_QC_COLLAB_093HORSE2FR301, MSM file

- 20111024_QE4_QC_COLLAB_093HORSE2FR301, raw file

Negative controls

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S52, MSM file

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S52, raw file

 

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S55, MSM file

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S55, raw file

 

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S60, MSM file

- 20110420_Velos1_JVO_COLLAB_Enrico-Ext-Ctrl_S60, raw file