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Triticum aestivum vs Triticum aestivum Arinalrfor LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Arinalrfor (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 Arinalrfor
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,414,084 alignment blocks

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

Uncovered: 2,204,856,521 out of 14,547,261,565
Covered: 12,342,405,044 out of 14,547,261,565

Uncovered: 3,868,478 out of 133,674,966
Matches: 128,634,003 out of 133,674,966
Mismatches: 1,059,833 out of 133,674,966
Insertions: 112,652 out of 133,674,966
Identity over aligned base-pairs: 99.1%

Triticum aestivum Arinalrfor

Uncovered: 2,278,262,092 out of 14,645,464,107
Covered: 12,367,202,015 out of 14,645,464,107

Uncovered: 10,512,127 out of 179,602,846
Matches: 167,426,523 out of 179,602,846
Mismatches: 1,525,668 out of 179,602,846
Insertions: 138,528 out of 179,602,846
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,414,084 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13,996
83.1 kb
10 bp - 100 bp
229,239
12.5 Mb
94,892
5.7 Mb
100 bp - 1 kb
488,187
183.9 Mb
225,307
80.9 Mb
1 kb - 10 kb
367,448
1.5 Gb
100,088
291.4 Mb
10 kb - 100 kb
303,815
9.5 Gb
5,595
103.8 Mb
100 kb - 1 Mb
11,399
1.5 Gb
474
167.2 Mb
1 Mb - 10 Mb
183
617.5 Mb
10 Mb - 100 Mb
23
495.0 Mb
100 Mb - 1 Gb
23
10.9 Gb