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Triticum aestivum vs Triticum aestivum Mace LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Mace (Triticum aestivum, PGSBv2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Triticum aestivum 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum aestivumTriticum aestivum Mace
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,537,258 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 2,154,662,385 out of 14,547,261,565
Covered: 12,392,599,180 out of 14,547,261,565

Uncovered: 2,643,245 out of 133,674,966
Matches: 129,760,231 out of 133,674,966
Mismatches: 1,143,497 out of 133,674,966
Insertions: 127,993 out of 133,674,966
Identity over aligned base-pairs: 99.0%

Triticum aestivum Mace

Uncovered: 1,984,100,080 out of 14,350,847,906
Covered: 12,366,747,826 out of 14,350,847,906

Uncovered: 8,047,472 out of 175,341,775
Matches: 165,627,352 out of 175,341,775
Mismatches: 1,527,939 out of 175,341,775
Insertions: 139,012 out of 175,341,775
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,537,258 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,094
90.1 kb
10 bp - 100 bp
246,094
13.5 Mb
101,375
6.1 Mb
100 bp - 1 kb
553,387
210.1 Mb
265,760
97.9 Mb
1 kb - 10 kb
402,576
1.6 Gb
126,050
342.1 Mb
10 kb - 100 kb
309,619
9.6 Gb
5,679
106.0 Mb
100 kb - 1 Mb
10,488
1.4 Gb
417
171.6 Mb
1 Mb - 10 Mb
198
626.4 Mb
10 Mb - 100 Mb
22
452.2 Mb
100 Mb - 1 Gb
21
10.9 Gb