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Arabidopsis thaliana vs Oryza barthii LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza barthii (Oryza barthii, O.barthii_v1) 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 barthii
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 110,934 alignment blocks

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

Uncovered: 93,878,831 out of 119,667,750
Covered: 25,788,919 out of 119,667,750

Uncovered: 14,744,635 out of 33,775,569
Matches: 12,346,021 out of 33,775,569
Mismatches: 6,307,169 out of 33,775,569
Insertions: 377,744 out of 33,775,569
Identity over aligned base-pairs: 64.9%

Oryza barthii

Uncovered: 280,400,139 out of 308,272,304
Covered: 27,872,165 out of 308,272,304

Uncovered: 20,267,981 out of 39,538,509
Matches: 12,427,083 out of 39,538,509
Mismatches: 6,390,299 out of 39,538,509
Insertions: 453,146 out of 39,538,509
Identity over aligned base-pairs: 64.5%

Block size distribution

Size range All 110,934 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
943
4.9 kb
10 bp - 100 bp
16,847
1.2 Mb
2,764
198.8 kb
100 bp - 1 kb
86,990
28.9 Mb
21,512
9.0 Mb
1 kb - 10 kb
6,154
8.9 Mb
14,061
29.3 Mb
10 kb - 100 kb
34
417.2 kb