Oryza sativa Japonica Group vs Prunus avium LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus avium (Prunus avium, PAV_r1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 GroupPrunus avium
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 140,371 alignment blocks

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

Uncovered: 341,410,849 out of 375,049,285
Covered: 33,638,436 out of 375,049,285

Uncovered: 13,869,338 out of 34,424,450
Matches: 13,341,413 out of 34,424,450
Mismatches: 6,733,073 out of 34,424,450
Insertions: 480,626 out of 34,424,450
Identity over aligned base-pairs: 64.9%

Prunus avium

Uncovered: 239,476,712 out of 272,361,615
Covered: 32,884,903 out of 272,361,615

Uncovered: 20,298,956 out of 38,693,511
Matches: 11,980,875 out of 38,693,511
Mismatches: 5,974,864 out of 38,693,511
Insertions: 438,816 out of 38,693,511
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 140,371 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,043
5.1 kb
10 bp - 100 bp
22,167
1.5 Mb
4,851
349.4 kb
100 bp - 1 kb
109,159
35.5 Mb
30,882
12.3 Mb
1 kb - 10 kb
7,998
12.1 Mb
16,760
35.8 Mb
10 kb - 100 kb
4
48.1 kb
60
767.5 kb