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Oryza longistaminata vs Oryza brachyantha LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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

ParameterOryza longistaminataOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 283,579 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 192,677,025 out of 326,442,508
Covered: 133,765,483 out of 326,442,508

Uncovered: 2,895,768 out of 34,512,301
Matches: 27,179,698 out of 34,512,301
Mismatches: 3,918,868 out of 34,512,301
Insertions: 517,967 out of 34,512,301
Identity over aligned base-pairs: 86.0%

Oryza brachyantha

Uncovered: 155,345,360 out of 260,838,168
Covered: 105,492,808 out of 260,838,168

Uncovered: 5,429,657 out of 33,473,466
Matches: 24,726,699 out of 33,473,466
Mismatches: 2,868,110 out of 33,473,466
Insertions: 449,000 out of 33,473,466
Identity over aligned base-pairs: 88.2%

Block size distribution

Size range All 283,579 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,752
24.0 kb
10 bp - 100 bp
49,085
3.1 Mb
20,363
1.4 Mb
100 bp - 1 kb
193,801
69.0 Mb
71,655
22.1 Mb
1 kb - 10 kb
36,938
70.6 Mb
9,309
24.3 Mb
10 kb - 100 kb
3
34.4 kb
2,036
67.0 Mb
100 kb - 1 Mb
172
27.9 Mb