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Arabidopsis thaliana vs Oryza glumipatula LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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 glumipatula
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 110,861 alignment blocks

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

Uncovered: 92,047,933 out of 119,667,750
Covered: 27,619,817 out of 119,667,750

Uncovered: 14,297,970 out of 33,775,569
Matches: 12,291,657 out of 33,775,569
Mismatches: 6,808,824 out of 33,775,569
Insertions: 377,118 out of 33,775,569
Identity over aligned base-pairs: 63.1%

Oryza glumipatula

Uncovered: 343,539,197 out of 372,860,283
Covered: 29,321,086 out of 372,860,283

Uncovered: 21,538,641 out of 41,246,944
Matches: 12,652,148 out of 41,246,944
Mismatches: 6,570,124 out of 41,246,944
Insertions: 486,031 out of 41,246,944
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 110,861 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
881
4.6 kb
10 bp - 100 bp
16,642
1.1 Mb
2,691
194.6 kb
100 bp - 1 kb
86,561
28.9 Mb
21,285
9.0 Mb
1 kb - 10 kb
6,729
10.9 Mb
14,548
30.8 Mb
10 kb - 100 kb
48
697.1 kb
109
1.6 Mb