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Arabidopsis thaliana vs Brassica rapa R-o-18 LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica rapa R-o-18 (Brassica rapa subsp. trilocularis, SCU_BraROA_2.3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. 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 rapa R-o-18
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 230,406 alignment blocks

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

Uncovered: 47,391,601 out of 119,667,750
Covered: 72,276,149 out of 119,667,750

Uncovered: 2,745,910 out of 33,775,569
Matches: 25,625,333 out of 33,775,569
Mismatches: 4,652,471 out of 33,775,569
Insertions: 751,855 out of 33,775,569
Identity over aligned base-pairs: 82.6%

Brassica rapa R-o-18

Uncovered: 242,840,713 out of 346,506,900
Covered: 103,666,187 out of 346,506,900

Uncovered: 15,743,083 out of 52,835,993
Matches: 31,132,655 out of 52,835,993
Mismatches: 5,421,954 out of 52,835,993
Insertions: 538,301 out of 52,835,993
Identity over aligned base-pairs: 83.9%

Block size distribution

Size range All 230,406 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,566
27.9 kb
10 bp - 100 bp
60,287
3.0 Mb
7,122
488.2 kb
100 bp - 1 kb
128,812
51.1 Mb
26,576
9.5 Mb
1 kb - 10 kb
36,731
68.2 Mb
7,123
15.7 Mb
10 kb - 100 kb
10
117.6 kb
213
6.4 Mb
100 kb - 1 Mb
86
27.5 Mb
1 Mb - 10 Mb
26
63.0 Mb