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Oryza rufipogon vs Oryza punctata LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) 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 punctata
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 364,762 alignment blocks

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

Uncovered: 139,479,600 out of 338,040,714
Covered: 198,561,114 out of 338,040,714

Uncovered: 1,707,062 out of 42,763,723
Matches: 37,341,253 out of 42,763,723
Mismatches: 3,006,143 out of 42,763,723
Insertions: 709,265 out of 42,763,723
Identity over aligned base-pairs: 91.0%

Oryza punctata

Uncovered: 229,098,676 out of 393,816,603
Covered: 164,717,927 out of 393,816,603

Uncovered: 4,445,870 out of 39,315,246
Matches: 32,634,630 out of 39,315,246
Mismatches: 1,833,928 out of 39,315,246
Insertions: 400,818 out of 39,315,246
Identity over aligned base-pairs: 93.6%

Block size distribution

Size range All 364,762 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,658
35.2 kb
10 bp - 100 bp
75,417
4.6 Mb
31,842
2.1 Mb
100 bp - 1 kb
232,157
82.3 Mb
81,683
28.0 Mb
1 kb - 10 kb
51,327
118.7 Mb
12,882
26.0 Mb
10 kb - 100 kb
203
2.4 Mb
239
5.4 Mb
100 kb - 1 Mb
17
2.9 Mb
1 Mb - 10 Mb
5
40.5 Mb
10 Mb - 100 Mb
7
103.0 Mb