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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-2A var. Gobol Sail) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-2A var. Gobol Sail) (Oryza sativa Indica Group, Os132424RS1) 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-2A var. Gobol Sail)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 119,464 alignment blocks

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

Uncovered: 68,338,640 out of 375,049,285
Covered: 306,710,645 out of 375,049,285

Uncovered: 323,833 out of 34,818,902
Matches: 34,096,546 out of 34,818,902
Mismatches: 332,117 out of 34,818,902
Insertions: 66,406 out of 34,818,902
Identity over aligned base-pairs: 98.8%

Oryza sativa (Xian/Indica-2A var. Gobol Sail)

Uncovered: 84,947,480 out of 392,847,014
Covered: 307,899,534 out of 392,847,014

Uncovered: 287,465 out of 41,956,946
Matches: 41,051,484 out of 41,956,946
Mismatches: 518,177 out of 41,956,946
Insertions: 99,820 out of 41,956,946
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 119,464 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,376
8.0 kb
10 bp - 100 bp
24,898
1.4 Mb
11,891
726.3 kb
100 bp - 1 kb
56,647
20.4 Mb
26,661
9.5 Mb
1 kb - 10 kb
27,351
98.4 Mb
7,801
18.1 Mb
10 kb - 100 kb
9,057
191.5 Mb
311
6.0 Mb
100 kb - 1 Mb
135
21.7 Mb
20
3.4 Mb
1 Mb - 10 Mb
1
3.0 Mb
10 Mb - 100 Mb
12
292.6 Mb