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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang) (Oryza sativa Indica Group, Os127518RS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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 GroupOryza sativa (Xian/Indica-3B1 var. Khao Yai Guang)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 120,515 alignment blocks

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

Uncovered: 68,532,243 out of 375,049,285
Covered: 306,517,042 out of 375,049,285

Uncovered: 326,355 out of 34,818,902
Matches: 34,107,845 out of 34,818,902
Mismatches: 318,879 out of 34,818,902
Insertions: 65,823 out of 34,818,902
Identity over aligned base-pairs: 98.9%

Oryza sativa (Xian/Indica-3B1 var. Khao Yai Guang)

Uncovered: 89,433,151 out of 399,249,348
Covered: 309,816,197 out of 399,249,348

Uncovered: 270,120 out of 42,343,724
Matches: 41,451,526 out of 42,343,724
Mismatches: 523,604 out of 42,343,724
Insertions: 98,474 out of 42,343,724
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 120,515 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,373
8.1 kb
10 bp - 100 bp
24,867
1.4 Mb
11,815
722.2 kb
100 bp - 1 kb
57,201
20.6 Mb
26,727
9.6 Mb
1 kb - 10 kb
27,805
99.9 Mb
7,989
18.4 Mb
10 kb - 100 kb
9,151
194.4 Mb
328
6.3 Mb
100 kb - 1 Mb
118
18.4 Mb
22
4.8 Mb
1 Mb - 10 Mb
1
3.1 Mb
10 Mb - 100 Mb
12
291.8 Mb