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Arabidopsis thaliana vs Brassica napus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 napus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 525,856 alignment blocks

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

Uncovered: 34,697,339 out of 119,667,750
Covered: 84,970,411 out of 119,667,750

Uncovered: 1,264,636 out of 33,775,569
Matches: 24,107,166 out of 33,775,569
Mismatches: 7,662,498 out of 33,775,569
Insertions: 741,269 out of 33,775,569
Identity over aligned base-pairs: 74.2%

Brassica napus

Uncovered: 552,713,876 out of 848,200,303
Covered: 295,486,427 out of 848,200,303

Uncovered: 7,894,629 out of 101,157,402
Matches: 77,965,998 out of 101,157,402
Mismatches: 13,984,775 out of 101,157,402
Insertions: 1,312,000 out of 101,157,402
Identity over aligned base-pairs: 83.6%

Block size distribution

Size range All 525,856 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,979
42.9 kb
10 bp - 100 bp
91,306
5.1 Mb
22,070
1.5 Mb
100 bp - 1 kb
328,902
131.9 Mb
110,515
42.0 Mb
1 kb - 10 kb
98,339
191.9 Mb
34,713
85.4 Mb
10 kb - 100 kb
328
9.7 Mb
2,091
64.9 Mb
100 kb - 1 Mb
2
202.7 kb
513
125.4 Mb
1 Mb - 10 Mb
14
19.5 Mb