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Oryza sativa Japonica Group vs Setaria viridis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Setaria viridis (Setaria viridis, Setaria_viridis_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 GroupSetaria viridis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 211,430 alignment blocks

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

Uncovered: 292,957,993 out of 375,049,285
Covered: 82,091,292 out of 375,049,285

Uncovered: 3,216,103 out of 34,424,450
Matches: 24,490,126 out of 34,424,450
Mismatches: 5,942,893 out of 34,424,450
Insertions: 775,328 out of 34,424,450
Identity over aligned base-pairs: 78.5%

Setaria viridis

Uncovered: 306,534,779 out of 395,731,502
Covered: 89,196,723 out of 395,731,502

Uncovered: 5,340,162 out of 41,880,594
Matches: 28,603,016 out of 41,880,594
Mismatches: 7,076,528 out of 41,880,594
Insertions: 860,888 out of 41,880,594
Identity over aligned base-pairs: 78.3%

Block size distribution

Size range All 211,430 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,889
10.3 kb
10 bp - 100 bp
32,883
2.1 Mb
13,002
902.0 kb
100 bp - 1 kb
144,505
54.6 Mb
53,074
17.8 Mb
1 kb - 10 kb
32,147
56.5 Mb
14,445
33.4 Mb
10 kb - 100 kb
6
73.9 kb
330
7.4 Mb
100 kb - 1 Mb
34
11.8 Mb
1 Mb - 10 Mb
13
42.0 Mb