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Arabidopsis thaliana vs Oryza punctata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) 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 punctata
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 112,119 alignment blocks

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

Uncovered: 93,545,811 out of 119,667,750
Covered: 26,121,939 out of 119,667,750

Uncovered: 14,466,129 out of 33,775,569
Matches: 12,534,555 out of 33,775,569
Mismatches: 6,382,154 out of 33,775,569
Insertions: 392,731 out of 33,775,569
Identity over aligned base-pairs: 64.9%

Oryza punctata

Uncovered: 364,961,555 out of 393,816,603
Covered: 28,855,048 out of 393,816,603

Uncovered: 19,081,200 out of 39,315,246
Matches: 13,007,337 out of 39,315,246
Mismatches: 6,727,290 out of 39,315,246
Insertions: 499,419 out of 39,315,246
Identity over aligned base-pairs: 64.3%

Block size distribution

Size range All 112,119 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
982
5.2 kb
10 bp - 100 bp
17,111
1.2 Mb
2,875
205.4 kb
100 bp - 1 kb
87,421
29.3 Mb
21,142
9.0 Mb
1 kb - 10 kb
6,605
9.6 Mb
14,598
30.4 Mb
10 kb - 100 kb
41
495.0 kb