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Arabidopsis thaliana vs Ostreococcus lucimarinus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901, ASM9206v1) 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 thalianaOstreococcus 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 11,176 alignment blocks

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

Uncovered: 117,450,957 out of 119,667,750
Covered: 2,216,793 out of 119,667,750

Uncovered: 31,705,252 out of 33,775,569
Matches: 1,290,726 out of 33,775,569
Mismatches: 733,466 out of 33,775,569
Insertions: 46,125 out of 33,775,569
Identity over aligned base-pairs: 62.3%

Ostreococcus lucimarinus

Uncovered: 11,936,367 out of 13,204,888
Covered: 1,268,521 out of 13,204,888

Uncovered: 7,997,677 out of 9,226,744
Matches: 764,452 out of 9,226,744
Mismatches: 443,286 out of 9,226,744
Insertions: 21,329 out of 9,226,744
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 11,176 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
44
248.0 bp
10 bp - 100 bp
3,067
227.7 kb
274
20.4 kb
100 bp - 1 kb
7,856
1.9 Mb
2,780
1.2 Mb
1 kb - 10 kb
209
295.0 kb
745
1.2 Mb