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Oryza sativa Japonica Group vs Oryza sativa Indica Group LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. 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)3000
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 GroupOryza sativa Indica Group
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 127,294 alignment blocks

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

Uncovered: 64,977,030 out of 375,049,285
Covered: 310,072,255 out of 375,049,285

Uncovered: 349,957 out of 34,818,902
Matches: 33,923,310 out of 34,818,902
Mismatches: 455,211 out of 34,818,902
Insertions: 90,424 out of 34,818,902
Identity over aligned base-pairs: 98.4%

Oryza sativa Indica Group

Uncovered: 143,812,226 out of 427,004,890
Covered: 283,192,664 out of 427,004,890

Uncovered: 6,417,323 out of 45,465,969
Matches: 38,706,848 out of 45,465,969
Mismatches: 277,779 out of 45,465,969
Insertions: 64,019 out of 45,465,969
Identity over aligned base-pairs: 99.1%

Block size distribution

Size range All 127,294 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,250
7.3 kb
10 bp - 100 bp
25,563
1.5 Mb
13,669
841.1 kb
100 bp - 1 kb
57,331
21.3 Mb
27,726
9.5 Mb
1 kb - 10 kb
34,395
122.2 Mb
8,850
23.5 Mb
10 kb - 100 kb
8,743
166.0 Mb
615
13.7 Mb
100 kb - 1 Mb
12
1.5 Mb
11
3.0 Mb
1 Mb - 10 Mb
1
1.0 Mb
10 Mb - 100 Mb
12
260.9 Mb