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Human vs Crab-eating macaque LastZ results

Human (Homo sapiens, GRCh38) and Crab-eating macaque (Macaca fascicularis, Macaca_fascicularis_6.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
Seed and Transition value (T)1
Scoring matrix (Q)
Primate:
    A    C    G    T
   90 -330 -236 -356
 -330  100 -318 -236
 -236 -318  100 -330
 -356 -236 -330   90

Chunking parameters

ParameterHumanCrab-eating macaque
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options

Statistics over 857,702 alignment blocks

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

Uncovered: 570,871,318 out of 3,099,750,718
Covered: 2,528,879,400 out of 3,099,750,718

Uncovered: 899,896 out of 38,571,754
Matches: 36,021,299 out of 38,571,754
Mismatches: 1,484,294 out of 38,571,754
Insertions: 166,265 out of 38,571,754
Identity over aligned base-pairs: 95.6%

Crab-eating macaque

Uncovered: 389,538,299 out of 2,906,155,132
Covered: 2,516,616,833 out of 2,906,155,132

Uncovered: 727,551 out of 34,070,036
Matches: 32,154,430 out of 34,070,036
Mismatches: 1,110,631 out of 34,070,036
Insertions: 77,424 out of 34,070,036
Identity over aligned base-pairs: 96.4%

Block size distribution

Size range All 857,702 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
19,596
108.8 kb
10 bp - 100 bp
85,362
4.4 Mb
27,969
1.7 Mb
100 bp - 1 kb
255,066
109.3 Mb
65,640
19.8 Mb
1 kb - 10 kb
435,965
1.6 Gb
12,902
38.1 Mb
10 kb - 100 kb
61,644
954.9 Mb
3,251
100.5 Mb
100 kb - 1 Mb
69
9.1 Mb
533
112.2 Mb
1 Mb - 10 Mb
21
52.4 Mb
10 Mb - 100 Mb
34
1.5 Gb
100 Mb - 1 Gb
7
879.1 Mb