We need your help! Has Ensembl saved you time or effort? Please take 15 minutes to fill in a survey and help EMBL-EBI make the case for why open data resources are critical to life science research.
https://www.surveymonkey.com/r/QGFMBH8?channel=[webpage]

 
Ensembl Home
More ▼
Search »
In this section
Related content

Cattle vs Hybrid - Bos Indicus LastZ results

Cattle (Bos taurus, ARS-UCD2.0) and Hybrid - Bos Indicus (Bos indicus x Bos taurus, UOA_Brahman_1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 114. Cattle was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterCattleHybrid - Bos Indicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 61,065 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Cattle

Uncovered: 126,265,781 out of 2,770,686,120
Covered: 2,644,420,339 out of 2,770,686,120

Uncovered: 578,106 out of 35,918,484
Matches: 35,228,308 out of 35,918,484
Mismatches: 104,656 out of 35,918,484
Insertions: 7,414 out of 35,918,484
Identity over aligned base-pairs: 99.7%

Hybrid - Bos Indicus

Uncovered: 75,772,298 out of 2,680,953,056
Covered: 2,605,180,758 out of 2,680,953,056

Uncovered: 594,340 out of 37,484,807
Matches: 36,785,400 out of 37,484,807
Mismatches: 96,647 out of 37,484,807
Insertions: 8,420 out of 37,484,807
Identity over aligned base-pairs: 99.7%

Block size distribution

Size range All 61,065 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
772
4.6 kb
10 bp - 100 bp
6,486
328.3 kb
1,922
114.8 kb
100 bp - 1 kb
12,754
4.9 Mb
4,591
1.7 Mb
1 kb - 10 kb
11,938
48.9 Mb
2,090
6.7 Mb
10 kb - 100 kb
20,685
862.8 Mb
753
22.0 Mb
100 kb - 1 Mb
8,422
1.7 Gb
80
19.2 Mb
1 Mb - 10 Mb
8
8.9 Mb
5
26.1 Mb
10 Mb - 100 Mb
19
1.2 Gb
100 Mb - 1 Gb
11
1.3 Gb