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Oryza sativa Japonica Group vs Brachypodium distachyon LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 GroupBrachypodium distachyon
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 175,305 alignment blocks

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

Uncovered: 294,783,826 out of 375,049,285
Covered: 80,265,459 out of 375,049,285

Uncovered: 3,560,443 out of 34,403,043
Matches: 24,107,053 out of 34,403,043
Mismatches: 5,921,149 out of 34,403,043
Insertions: 814,398 out of 34,403,043
Identity over aligned base-pairs: 78.2%

Brachypodium distachyon

Uncovered: 194,458,588 out of 271,163,419
Covered: 76,704,831 out of 271,163,419

Uncovered: 4,894,871 out of 39,007,317
Matches: 26,768,657 out of 39,007,317
Mismatches: 6,518,372 out of 39,007,317
Insertions: 825,417 out of 39,007,317
Identity over aligned base-pairs: 78.5%

Block size distribution

Size range All 175,305 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,508
8.9 kb
10 bp - 100 bp
25,090
1.6 Mb
9,061
632.1 kb
100 bp - 1 kb
118,695
47.0 Mb
36,324
12.4 Mb
1 kb - 10 kb
30,004
52.5 Mb
12,194
28.8 Mb
10 kb - 100 kb
8
114.5 kb
335
7.9 Mb
100 kb - 1 Mb
25
7.9 Mb
1 Mb - 10 Mb
11
43.6 Mb