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Oryza sativa Japonica Group vs Ostreococcus lucimarinus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901, ASM9206v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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)
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 sativa Japonica GroupOstreococcus lucimarinus
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 12,496 alignment blocks

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

Uncovered: 372,518,183 out of 375,049,285
Covered: 2,531,102 out of 375,049,285

Uncovered: 32,311,523 out of 34,403,043
Matches: 1,320,382 out of 34,403,043
Mismatches: 718,480 out of 34,403,043
Insertions: 52,658 out of 34,403,043
Identity over aligned base-pairs: 63.1%

Ostreococcus lucimarinus

Uncovered: 11,712,469 out of 13,204,888
Covered: 1,492,419 out of 13,204,888

Uncovered: 7,840,072 out of 9,226,744
Matches: 866,911 out of 9,226,744
Mismatches: 483,240 out of 9,226,744
Insertions: 36,521 out of 9,226,744
Identity over aligned base-pairs: 62.5%

Block size distribution

Size range All 12,496 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
49
296.0 bp
10 bp - 100 bp
3,432
253.2 kb
574
41.1 kb
100 bp - 1 kb
8,705
2.1 Mb
3,637
1.5 Mb
1 kb - 10 kb
310
448.5 kb
809
1.3 Mb