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Arabidopsis thaliana vs Brassica juncea LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica juncea (Brassica juncea, ASM1870372v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 108. Arabidopsis thaliana 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

ParameterArabidopsis thalianaBrassica juncea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 467,015 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 42,372,607 out of 119,667,750
Covered: 77,295,143 out of 119,667,750

Uncovered: 2,253,995 out of 33,775,569
Matches: 26,041,769 out of 33,775,569
Mismatches: 4,742,180 out of 33,775,569
Insertions: 737,625 out of 33,775,569
Identity over aligned base-pairs: 82.6%

Brassica juncea

Uncovered: 710,955,868 out of 933,495,403
Covered: 222,539,535 out of 933,495,403

Uncovered: 17,388,849 out of 78,121,651
Matches: 50,796,280 out of 78,121,651
Mismatches: 9,013,271 out of 78,121,651
Insertions: 923,251 out of 78,121,651
Identity over aligned base-pairs: 83.6%

Block size distribution

Size range All 467,015 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9,850
57.9 kb
10 bp - 100 bp
121,445
5.9 Mb
15,534
1.1 Mb
100 bp - 1 kb
261,114
103.0 Mb
65,264
24.1 Mb
1 kb - 10 kb
74,576
142.2 Mb
17,136
37.9 Mb
10 kb - 100 kb
30
645.5 kb
450
13.7 Mb
100 kb - 1 Mb
161
53.9 Mb
1 Mb - 10 Mb
55
121.2 Mb