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Oryza rufipogon vs Oryza brachyantha LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza rufipogon 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 rufipogonOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 271,668 alignment blocks

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

Uncovered: 205,609,686 out of 338,040,714
Covered: 132,431,028 out of 338,040,714

Uncovered: 5,331,285 out of 42,763,723
Matches: 31,739,058 out of 42,763,723
Mismatches: 4,816,950 out of 42,763,723
Insertions: 876,430 out of 42,763,723
Identity over aligned base-pairs: 84.8%

Oryza brachyantha

Uncovered: 152,659,456 out of 260,838,168
Covered: 108,178,712 out of 260,838,168

Uncovered: 4,314,228 out of 33,473,466
Matches: 25,833,810 out of 33,473,466
Mismatches: 2,885,948 out of 33,473,466
Insertions: 439,480 out of 33,473,466
Identity over aligned base-pairs: 88.6%

Block size distribution

Size range All 271,668 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,968
25.5 kb
10 bp - 100 bp
48,352
3.0 Mb
19,977
1.4 Mb
100 bp - 1 kb
181,454
64.8 Mb
60,241
17.6 Mb
1 kb - 10 kb
37,886
73.5 Mb
6,511
15.0 Mb
10 kb - 100 kb
8
87.0 kb
178
4.0 Mb
100 kb - 1 Mb
5
594.7 kb
1 Mb - 10 Mb
9
60.0 Mb
10 Mb - 100 Mb
3
42.8 Mb