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Chicken vs Abingdon island giant tortoise LastZ results

Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Abingdon island giant tortoise (Chelonoidis abingdonii, ASM359739v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 107. Chicken 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)3000
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

ParameterChickenAbingdon island giant tortoise
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 545,075 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Chicken

Uncovered: 712,977,112 out of 1,053,332,251
Covered: 340,355,139 out of 1,053,332,251

Uncovered: 4,558,133 out of 31,304,036
Matches: 21,643,279 out of 31,304,036
Mismatches: 4,922,731 out of 31,304,036
Insertions: 179,893 out of 31,304,036
Identity over aligned base-pairs: 80.9%

Abingdon island giant tortoise

Uncovered: 1,949,449,404 out of 2,300,739,315
Covered: 351,289,911 out of 2,300,739,315

Uncovered: 6,762,289 out of 29,396,458
Matches: 18,411,211 out of 29,396,458
Mismatches: 3,977,877 out of 29,396,458
Insertions: 245,081 out of 29,396,458
Identity over aligned base-pairs: 81.3%

Block size distribution

Size range All 545,075 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,966
13.3 kb
10 bp - 100 bp
29,613
1.8 Mb
2,634
191.0 kb
100 bp - 1 kb
400,107
186.4 Mb
20,116
8.2 Mb
1 kb - 10 kb
113,360
184.3 Mb
8,260
22.3 Mb
10 kb - 100 kb
29
396.0 kb
1,855
67.9 Mb
100 kb - 1 Mb
1,005
254.6 Mb
1 Mb - 10 Mb
15
19.8 Mb