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Oryza sativa Japonica Group vs Daucus carota LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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
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 GroupDaucus carota
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 159,297 alignment blocks

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

Uncovered: 343,431,734 out of 375,049,285
Covered: 31,617,551 out of 375,049,285

Uncovered: 14,985,804 out of 34,403,043
Matches: 12,502,385 out of 34,403,043
Mismatches: 6,467,874 out of 34,403,043
Insertions: 446,980 out of 34,403,043
Identity over aligned base-pairs: 64.4%

Daucus carota

Uncovered: 384,509,919 out of 421,502,825
Covered: 36,992,906 out of 421,502,825

Uncovered: 15,930,827 out of 38,118,360
Matches: 14,427,445 out of 38,118,360
Mismatches: 7,329,232 out of 38,118,360
Insertions: 430,856 out of 38,118,360
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 159,297 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,138
5.6 kb
10 bp - 100 bp
26,212
1.8 Mb
6,659
472.8 kb
100 bp - 1 kb
124,379
39.2 Mb
37,637
14.4 Mb
1 kb - 10 kb
7,566
11.1 Mb
17,958
36.7 Mb
10 kb - 100 kb
2
23.9 kb
43
633.0 kb