Human vs Chinese softshell turtle LastZ results

Human (Homo sapiens, GRCh38) and Chinese softshell turtle (Pelodiscus sinensis, PelSin_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 76. Human 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

ParameterHumanChinese softshell turtle
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 327,091 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Human

Uncovered: 3,000,501,572 out of 3,096,649,726
Covered: 96,148,154 out of 3,096,649,726

Uncovered: 8,149,893 out of 35,228,305
Matches: 20,087,300 out of 35,228,305
Mismatches: 6,645,385 out of 35,228,305
Insertions: 345,727 out of 35,228,305
Identity over aligned base-pairs: 74.2%

Chinese softshell turtle

Uncovered: 2,122,163,785 out of 2,202,483,752
Covered: 80,319,967 out of 2,202,483,752

Uncovered: 6,786,200 out of 28,389,223
Matches: 16,236,520 out of 28,389,223
Mismatches: 5,121,617 out of 28,389,223
Insertions: 244,886 out of 28,389,223
Identity over aligned base-pairs: 75.2%

Block size distribution

Size range All 327,091 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
703
3.5 kb
10 bp - 100 bp
40,993
3.0 Mb
14,957
1.1 Mb
100 bp - 1 kb
273,320
78.7 Mb
122,906
42.4 Mb
1 kb - 10 kb
12,072
18.8 Mb
17,616
39.0 Mb
10 kb - 100 kb
3
45.8 kb
602
13.1 Mb
100 kb - 1 Mb
31
5.1 Mb