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Oryza longistaminata vs Oryza sativa Indica Group LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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
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 longistaminataOryza sativa Indica Group
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 322,566 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 75,195,824 out of 326,442,508
Covered: 251,246,684 out of 326,442,508

Uncovered: 1,165,532 out of 34,512,301
Matches: 32,095,565 out of 34,512,301
Mismatches: 1,082,217 out of 34,512,301
Insertions: 168,987 out of 34,512,301
Identity over aligned base-pairs: 96.2%

Oryza sativa Indica Group

Uncovered: 212,523,064 out of 427,004,890
Covered: 214,481,826 out of 427,004,890

Uncovered: 11,711,034 out of 45,465,969
Matches: 32,480,592 out of 45,465,969
Mismatches: 1,030,908 out of 45,465,969
Insertions: 243,435 out of 45,465,969
Identity over aligned base-pairs: 96.2%

Block size distribution

Size range All 322,566 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,107
24.8 kb
10 bp - 100 bp
64,506
3.8 Mb
31,357
2.0 Mb
100 bp - 1 kb
186,052
68.7 Mb
76,519
25.7 Mb
1 kb - 10 kb
66,841
170.5 Mb
16,644
40.5 Mb
10 kb - 100 kb
1,060
13.5 Mb
3,142
108.7 Mb
100 kb - 1 Mb
473
79.7 Mb