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Oryza sativa Japonica Group vs Eragrostis curvula LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Eragrostis curvula (Eragrostis curvula, CERZOS_E.curvula1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 GroupEragrostis curvula
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options

Statistics over 305,247 alignment blocks

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

Uncovered: 292,702,115 out of 375,049,285
Covered: 82,347,170 out of 375,049,285

Uncovered: 3,121,884 out of 34,818,902
Matches: 24,638,076 out of 34,818,902
Mismatches: 6,216,224 out of 34,818,902
Insertions: 842,718 out of 34,818,902
Identity over aligned base-pairs: 77.7%

Eragrostis curvula

Uncovered: 469,300,689 out of 603,072,269
Covered: 133,771,580 out of 603,072,269

Uncovered: 10,860,649 out of 62,628,176
Matches: 39,357,874 out of 62,628,176
Mismatches: 11,103,867 out of 62,628,176
Insertions: 1,305,786 out of 62,628,176
Identity over aligned base-pairs: 76.0%

Block size distribution

Size range All 305,247 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,676
14.6 kb
10 bp - 100 bp
46,697
3.0 Mb
20,363
1.4 Mb
100 bp - 1 kb
210,543
79.9 Mb
77,102
25.9 Mb
1 kb - 10 kb
45,330
77.9 Mb
24,389
57.0 Mb
10 kb - 100 kb
1
10.2 kb
1,039
24.2 Mb
100 kb - 1 Mb
41
14.7 Mb
1 Mb - 10 Mb
18
37.5 Mb