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Oryza sativa Japonica Group vs Oryza brachyantha LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. 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)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 sativa Japonica GroupOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 306,220 alignment blocks

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

Uncovered: 227,820,373 out of 375,049,285
Covered: 147,228,912 out of 375,049,285

Uncovered: 2,642,069 out of 34,818,902
Matches: 27,643,273 out of 34,818,902
Mismatches: 3,867,982 out of 34,818,902
Insertions: 665,578 out of 34,818,902
Identity over aligned base-pairs: 85.9%

Oryza brachyantha

Uncovered: 150,356,678 out of 260,838,168
Covered: 110,481,490 out of 260,838,168

Uncovered: 4,128,413 out of 33,473,466
Matches: 25,976,553 out of 33,473,466
Mismatches: 2,926,946 out of 33,473,466
Insertions: 441,554 out of 33,473,466
Identity over aligned base-pairs: 88.5%

Block size distribution

Size range All 306,220 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,087
26.2 kb
10 bp - 100 bp
55,740
3.4 Mb
25,243
1.7 Mb
100 bp - 1 kb
204,646
72.5 Mb
78,799
24.0 Mb
1 kb - 10 kb
41,737
80.9 Mb
9,876
23.2 Mb
10 kb - 100 kb
10
110.9 kb
169
3.6 Mb
100 kb - 1 Mb
4
524.1 kb
1 Mb - 10 Mb
9
60.7 Mb
10 Mb - 100 Mb
3
43.2 Mb