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Oryza sativa Japonica Group vs Saccharum spontaneum LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 GroupSaccharum spontaneum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,188,926 alignment blocks

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

Uncovered: 288,024,182 out of 375,049,285
Covered: 87,025,103 out of 375,049,285

Uncovered: 3,169,294 out of 34,424,450
Matches: 24,283,289 out of 34,424,450
Mismatches: 6,159,489 out of 34,424,450
Insertions: 812,378 out of 34,424,450
Identity over aligned base-pairs: 77.7%

Saccharum spontaneum

Uncovered: 2,433,851,903 out of 2,900,240,836
Covered: 466,388,933 out of 2,900,240,836

Uncovered: 8,744,370 out of 62,027,027
Matches: 41,836,323 out of 62,027,027
Mismatches: 10,149,562 out of 62,027,027
Insertions: 1,296,772 out of 62,027,027
Identity over aligned base-pairs: 78.5%

Block size distribution

Size range All 1,188,926 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8,482
44.7 kb
10 bp - 100 bp
197,759
12.8 Mb
105,802
7.4 Mb
100 bp - 1 kb
856,718
288.4 Mb
465,347
143.1 Mb
1 kb - 10 kb
125,956
215.2 Mb
89,133
229.8 Mb
10 kb - 100 kb
11
152.1 kb
3,787
70.9 Mb
100 kb - 1 Mb
80
24.3 Mb
1 Mb - 10 Mb
25
41.2 Mb