Milvus milvus

red kite

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


metadata.yaml (view) (edit on github)
species:
  short_name: bMilMil
  name: Milvus milvus
  taxon_id: 43518
  common_name: red kite
  order:
    name: Accipitriformes
  family:
    name: Accipitridae
  individuals:
    - short_name: bMilMil1
      biosample_id: SAMEA115765510
      sex:
  genome_size: 1467000000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bMilMil3 74.82 Gbp 51.00x 33.4 GiB
PacBio HiFi (.fq) bMilMil3 81.35 Gbp 55.45x 40.6 GiB
PacBio HiFi (.bam) bMilMil1 94.29 Gbp 64.27x 29.4 GiB
bMilMil3 5.19 Gbp 3.54x 3.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.47 Gbp.
Last upload on 9 September 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMilMil1 PacBio HiFi (.bam) 94.29 Gbp 64.27x 29.4 GiB
bMilMil3 PacBio HiFi (subreads) 74.82 Gbp 51.00x 33.4 GiB
PacBio HiFi (.fq) 81.35 Gbp 55.45x 40.6 GiB
PacBio HiFi (.bam) 5.19 Gbp 3.54x 3.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.47 Gbp.
Last upload on 9 September 2025.
Assemblies
Individual 3 Primary Assembly
Version assembly_vogelwarte from 17 November 2025
bMilMil3.pri.cur.20251117.fasta.gz (366.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 46.82 Mbp 2 85.65 Mbp
20 6 37.28 Mbp 4 76.23 Mbp
30 11 28.64 Mbp 7 47.72 Mbp
40 16 25.16 Mbp 10 44.63 Mbp
50 23 22.51 Mbp 13 42.11 Mbp
60 31 14.88 Mbp 17 33.80 Mbp
70 43 9.99 Mbp 22 29.57 Mbp
80 68 3.40 Mbp 27 23.86 Mbp
90 0 0
100 0 0
0.884x 347 1.30 Gbp 243 1.30 Gbp
NG based on genome size 1.47 Gbp.
Individual 3 Alternate Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 5 May 2026
bMilMil3.HiC.hap1.20260505.fasta.gz (341.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 42.42 Mbp 2 87.48 Mbp
20 7 37.33 Mbp 4 77.33 Mbp
30 12 29.92 Mbp 6 50.64 Mbp
40 17 24.77 Mbp 10 45.03 Mbp
50 24 21.16 Mbp 13 42.50 Mbp
60 31 17.28 Mbp 17 34.45 Mbp
70 42 10.24 Mbp 21 30.94 Mbp
80 61 5.24 Mbp 26 23.97 Mbp
90 217 68.43 Kbp 117 85.97 Kbp
100 0 0
0.903x 304 1.32 Gbp 195 1.32 Gbp
NG based on genome size 1.47 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 5 May 2026
bMilMil3.HiC.hap2.20260505.fasta.gz (309.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 40.95 Mbp 2 80.60 Mbp
20 8 31.61 Mbp 4 54.67 Mbp
30 12 29.34 Mbp 7 46.89 Mbp
40 18 22.67 Mbp 11 43.97 Mbp
50 26 17.11 Mbp 14 38.72 Mbp
60 36 12.32 Mbp 19 30.12 Mbp
70 51 7.51 Mbp 24 23.84 Mbp
80 143 193.32 Kbp 61 296.66 Kbp
90 0 0
100 0 0
0.806x 239 1.18 Gbp 144 1.18 Gbp
NG based on genome size 1.47 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/bMilMil3.yml (view)
species: Milvus milvus
specimen: bMilMil3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Milvus_milvus/bMilMil3/assembly_vgp_HiC_2.0/bMilMil3.HiC.hap1.20260505.fasta.gz
hap2: s3://genomeark/species/Milvus_milvus/bMilMil3/assembly_vgp_HiC_2.0/bMilMil3.HiC.hap2.20260505.fasta.gz
pretext_hap1: s3://genomeark/species/Milvus_milvus/bMilMil3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bMilMil3_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Milvus_milvus/bMilMil3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bMilMil3_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Milvus_milvus/bMilMil3/assembly_vgp_HiC_2.0/evaluation/merqury/bMilMil3_png/
pacbio_read_dir: s3://genomeark/species/Milvus_milvus/bMilMil3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Milvus_milvus/bMilMil3/genomic_data/HiC/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP1 genomic profiling workflow (v20260331 update)
  - VGP4 HiFi HiC assembly workflow (v0.6) Did not trim HiC reads (Arima v1).
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of bMilMil3 resulting in two haplotype assemblies.
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.