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Oryza nivara vs Oryza brachyantha LastZ results

Oryza nivara (Oryza nivara, Oryza_nivara_v1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza nivara 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

ParameterOryza nivaraOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 262,679 alignment blocks

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

Uncovered: 206,368,317 out of 337,950,324
Covered: 131,582,007 out of 337,950,324

Uncovered: 5,035,722 out of 42,562,444
Matches: 31,813,973 out of 42,562,444
Mismatches: 4,834,301 out of 42,562,444
Insertions: 878,448 out of 42,562,444
Identity over aligned base-pairs: 84.8%

Oryza brachyantha

Uncovered: 152,988,685 out of 260,838,168
Covered: 107,849,483 out of 260,838,168

Uncovered: 4,420,110 out of 33,473,466
Matches: 25,749,276 out of 33,473,466
Mismatches: 2,869,863 out of 33,473,466
Insertions: 434,217 out of 33,473,466
Identity over aligned base-pairs: 88.6%

Block size distribution

Size range All 262,679 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,841
24.9 kb
10 bp - 100 bp
44,816
2.7 Mb
17,762
1.2 Mb
100 bp - 1 kb
175,888
63.5 Mb
57,485
17.0 Mb
1 kb - 10 kb
38,124
74.1 Mb
6,807
16.7 Mb
10 kb - 100 kb
10
110.7 kb
488
13.2 Mb
100 kb - 1 Mb
35
5.3 Mb
1 Mb - 10 Mb
9
49.9 Mb
10 Mb - 100 Mb
3
37.2 Mb