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Oryza sativa Japonica Group vs Brassica napus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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)
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 GroupBrassica napus
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 311,135 alignment blocks

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

Uncovered: 337,406,533 out of 375,049,285
Covered: 37,642,752 out of 375,049,285

Uncovered: 14,357,048 out of 34,403,043
Matches: 12,474,343 out of 34,403,043
Mismatches: 6,954,670 out of 34,403,043
Insertions: 616,982 out of 34,403,043
Identity over aligned base-pairs: 62.2%

Brassica napus

Uncovered: 761,084,360 out of 848,200,303
Covered: 87,115,943 out of 848,200,303

Uncovered: 43,320,793 out of 101,157,402
Matches: 38,081,154 out of 101,157,402
Mismatches: 18,702,347 out of 101,157,402
Insertions: 1,053,108 out of 101,157,402
Identity over aligned base-pairs: 65.8%

Block size distribution

Size range All 311,135 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,547
13.2 kb
10 bp - 100 bp
50,814
3.5 Mb
10,202
733.5 kb
100 bp - 1 kb
241,844
78.6 Mb
70,175
28.6 Mb
1 kb - 10 kb
15,830
24.4 Mb
37,425
75.9 Mb
10 kb - 100 kb
99
3.0 Mb
151
3.8 Mb
100 kb - 1 Mb
1
102.2 kb
4
489.0 kb