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Arabidopsis thaliana vs Oryza rufipogon LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Arabidopsis thaliana 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)
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

ParameterArabidopsis thalianaOryza rufipogon
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 113,206 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,573,917 out of 119,667,750
Covered: 26,093,833 out of 119,667,750

Uncovered: 14,489,656 out of 33,775,569
Matches: 12,521,884 out of 33,775,569
Mismatches: 6,379,404 out of 33,775,569
Insertions: 384,625 out of 33,775,569
Identity over aligned base-pairs: 64.9%

Oryza rufipogon

Uncovered: 309,346,329 out of 338,040,714
Covered: 28,694,385 out of 338,040,714

Uncovered: 22,634,884 out of 42,763,723
Matches: 12,914,679 out of 42,763,723
Mismatches: 6,715,139 out of 42,763,723
Insertions: 499,021 out of 42,763,723
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 113,206 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
965
5.1 kb
10 bp - 100 bp
17,307
1.2 Mb
2,920
209.8 kb
100 bp - 1 kb
88,594
29.4 Mb
22,057
9.2 Mb
1 kb - 10 kb
6,340
9.2 Mb
14,452
29.9 Mb
10 kb - 100 kb
35
432.6 kb