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Human vs Hybrid - Bos Indicus LastZ results

Human (Homo sapiens, GRCh38) and Hybrid - Bos Indicus (Bos indicus x Bos taurus, UOA_Brahman_1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 97. Human 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
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

ParameterHumanHybrid - Bos Indicus
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,369,904 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Human

Uncovered: 1,658,237,553 out of 3,099,750,718
Covered: 1,441,513,165 out of 3,099,750,718

Uncovered: 1,702,647 out of 38,571,754
Matches: 31,393,744 out of 38,571,754
Mismatches: 5,007,621 out of 38,571,754
Insertions: 467,742 out of 38,571,754
Identity over aligned base-pairs: 85.1%

Hybrid - Bos Indicus

Uncovered: 1,327,852,350 out of 2,680,953,056
Covered: 1,353,100,706 out of 2,680,953,056

Uncovered: 4,463,926 out of 37,484,807
Matches: 28,632,208 out of 37,484,807
Mismatches: 4,177,932 out of 37,484,807
Insertions: 210,741 out of 37,484,807
Identity over aligned base-pairs: 86.7%

Block size distribution

Size range All 2,369,904 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
82,917
553.8 kb
10 bp - 100 bp
287,912
14.1 Mb
17,259
1.2 Mb
100 bp - 1 kb
1,515,819
672.3 Mb
58,841
21.2 Mb
1 kb - 10 kb
482,598
858.5 Mb
18,427
45.3 Mb
10 kb - 100 kb
655
9.7 Mb
1,682
43.7 Mb
100 kb - 1 Mb
3
339.3 kb
229
62.1 Mb
1 Mb - 10 Mb
89
336.9 Mb
10 Mb - 100 Mb
49
1.0 Gb