Oryza sativa Japonica Group vs Olea europaea var. sylvestris LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Olea europaea var. sylvestris (Olea europaea var. sylvestris, O_europaea_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Oryza sativa Japonica Group 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)
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

ParameterOryza sativa Japonica GroupOlea europaea var. sylvestris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 207,550 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 337,411,441 out of 375,049,285
Covered: 37,637,844 out of 375,049,285

Uncovered: 14,644,201 out of 34,424,450
Matches: 12,245,906 out of 34,424,450
Mismatches: 7,084,853 out of 34,424,450
Insertions: 449,490 out of 34,424,450
Identity over aligned base-pairs: 61.9%

Olea europaea var. sylvestris

Uncovered: 1,090,013,901 out of 1,140,989,389
Covered: 50,975,488 out of 1,140,989,389

Uncovered: 26,906,376 out of 52,755,300
Matches: 16,898,571 out of 52,755,300
Mismatches: 8,448,984 out of 52,755,300
Insertions: 501,369 out of 52,755,300
Identity over aligned base-pairs: 65.4%

Block size distribution

Size range All 207,550 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,424
6.8 kb
10 bp - 100 bp
37,216
2.6 Mb
12,810
929.1 kb
100 bp - 1 kb
158,641
48.6 Mb
57,879
21.2 Mb
1 kb - 10 kb
10,158
18.6 Mb
21,970
45.6 Mb
10 kb - 100 kb
111
1.5 Mb
229
3.6 Mb