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Oryza longistaminata vs Oryza rufipogon LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) 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 rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 263,364 alignment blocks

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

Uncovered: 87,603,496 out of 326,442,508
Covered: 238,839,012 out of 326,442,508

Uncovered: 868,270 out of 34,512,301
Matches: 32,455,574 out of 34,512,301
Mismatches: 1,027,417 out of 34,512,301
Insertions: 161,040 out of 34,512,301
Identity over aligned base-pairs: 96.5%

Oryza rufipogon

Uncovered: 126,670,012 out of 338,040,714
Covered: 211,370,702 out of 338,040,714

Uncovered: 7,551,780 out of 42,763,723
Matches: 33,903,612 out of 42,763,723
Mismatches: 1,036,850 out of 42,763,723
Insertions: 271,481 out of 42,763,723
Identity over aligned base-pairs: 96.3%

Block size distribution

Size range All 263,364 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,511
21.9 kb
10 bp - 100 bp
43,157
2.5 Mb
17,867
1.1 Mb
100 bp - 1 kb
152,600
61.0 Mb
48,095
19.1 Mb
1 kb - 10 kb
62,935
164.8 Mb
12,124
29.4 Mb
10 kb - 100 kb
1,161
15.1 Mb
3,060
110.1 Mb
100 kb - 1 Mb
491
83.8 Mb