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Oryza sativa Japonica Group vs Lolium perenne LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Lolium perenne (Lolium perenne, MPB_Lper_Kyuss_1697) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 108. 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 GroupLolium perenne
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 254,048 alignment blocks

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

Uncovered: 296,160,685 out of 375,049,285
Covered: 78,888,600 out of 375,049,285

Uncovered: 3,680,832 out of 34,424,450
Matches: 23,850,644 out of 34,424,450
Mismatches: 6,036,367 out of 34,424,450
Insertions: 856,607 out of 34,424,450
Identity over aligned base-pairs: 77.6%

Lolium perenne

Uncovered: 2,168,503,383 out of 2,276,788,877
Covered: 108,285,494 out of 2,276,788,877

Uncovered: 11,095,027 out of 47,191,806
Matches: 27,915,851 out of 47,191,806
Mismatches: 7,332,053 out of 47,191,806
Insertions: 848,875 out of 47,191,806
Identity over aligned base-pairs: 77.3%

Block size distribution

Size range All 254,048 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,969
11.1 kb
10 bp - 100 bp
36,427
2.3 Mb
16,214
1.1 Mb
100 bp - 1 kb
177,942
67.6 Mb
78,082
27.5 Mb
1 kb - 10 kb
37,707
64.5 Mb
30,096
73.3 Mb
10 kb - 100 kb
3
33.5 kb
1,399
28.9 Mb
100 kb - 1 Mb
20
3.7 Mb