Benchmarks¶
Below are some benchmarks measuring Genozip’s performance on a variety of file types. In the case of BAM, CRAM, FASTQ and VCF, Genozip is shown here compressing already-compressed files.
To see more, peer-reviewed, benchmarks, see Publications.
As can be appreciated from the detailed compression reports following the table, the compression gains strongly depend on the specific fields contained in a file, and can therefore vary significantly.
Details |
Type |
Size |
.gz Size |
.genozip |
Genozip gain |
Gain vs .gz |
Data |
Link to data |
|---|---|---|---|---|---|---|---|---|
FASTQ (Illumina) |
294.7 GB |
61.2 GB |
13.5 GB |
21.8X |
4.5X |
30x Illumina NovaSeq (R1+R2) |
Unpublished |
|
FASTQ (Nanopore) |
538 MB |
268 MB |
169.5 MB |
3.2X |
1.6X |
Nanopore (virus) 1 |
||
FASTQ (BGI) |
265.5 GB |
99.9 GB |
48.8 MB |
5.4X |
2.0X |
DNBSEQ-G400 (R1+R2) |
||
BAM (Illumina) |
41 GB |
10 GB |
4.1X |
30x Illumina NovaSeq + Dragen |
Unpublished |
|||
BAM (PacBio CLR) |
53.8 GB |
28 GB |
1.9X |
PacBio CLR (mapped) |
||||
BAM (PacBio CCS) |
73.8 GB |
38.7 GB |
1.9X |
PacBio CCS + Winnowmap (mapped) |
||||
BAM (Nanopore) |
384.1 GB |
209.3 GB |
1.8X |
Nanopore + Winnowmap (mapped) |
||||
CRAM (Illumina) |
15 GB |
9.8 GB |
1.5X |
Illumina NovaSeq + bwa mem |
||||
VCF |
175.3 GB |
27 GB |
7.8 GB |
22.4X |
3.3X |
3202 human samples |
||
VCF |
1.2 TB |
132.4 GB |
31.6 GB |
37.9X |
4.2X |
1135 plant samples |
||
VCF |
26 GB |
1.9 GB |
315.5 MB |
84.3X |
6.2X |
Rice |
||
FASTA |
1.2 GB |
254.9 MB |
1.5 MB |
838.4X |
170X |
Covid-19 multi-FASTA 2 |
||
GFF3 |
3.7 GB |
91.8 MB |
32.3 MB |
117.9X |
2.8X |
Gene annotation |
||
23andMe |
23.6 MB |
4.2 MB |
5.7X |
Consumer DNA test “raw data” |
Unpublished |
|||
LOCS (Illumina) |
32 MB |
12MB |
5.9 KB |
5430X |
2006X |
Illumina s.locs file |
||
LOCS (Illumina) |
6.2 MB |
4.4MB |
3.3 MB |
1.9X |
1.3X |
Illumina s_X_XXXX.locs file |
Notes:
The tests were conducted with the
--bestoption. For BAM, CRAM, Illumina FASTQ files, the--referenceoption was used to specify the appropriate reference file. For Illumina FASTQ, the--pairoption was used.1 the data was converted to fastq with
fastq-dumpand compressed to .gz withbgzip. genozip was used with the--multiseqoption.2 the data was unzipped with
unzipand then compressed to .gz withbgzip. genozip was used with the--multiseqoption.
Detailed compression reports
The following reports can be produced during compression with genozip --stats or after compression with genocat --stats <myfile>.genozip.
FASTQ - 30x Illumina NovaSeq
FASTQ files (paired): <redacted>_R1_001.fastq.gz <redacted>_R2_001.fastq.gz
Reference: hs37d5.ref.genozip
Sequences: 860,000,926 Dictionaries: 36 Vblocks: 590 x 512 MB Sections: 10823
Read name style: Illumina-fastq
Genozip version: 13.0.6 github
Date compressed: 2021-12-08 00:49:27 ACDT
Command line: genozip --best --pair -ft -e hs37d5.ref.genozip --stats <redacted>_R1_001.fastq.gz <redacted>_R2_001.fastq.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 7.7 GB 56.9% 118.7 GB 40.3% 15.4X
SEQ 5.2 GB 38.1% 118.7 GB 40.3% 23.0X
DESC 682.4 MB 4.9% 52.4 GB 17.8% 78.7X
Other 71.1 KB 0.0% 4.8 GB 1.6% 70888.0X
LINE3 23.6 KB 0.0% - 0.0% 0.0X
GENOZIP vs BGZF 13.5 GB 100.0% 61.2 GB 100.0% 4.5X
GENOZIP vs TXT 13.5 GB 100.0% 294.7 GB 100.0% 21.8X
FASTQ - Nanopore virus data
FASTQ file: ERR2708427.1.fastq.gz
Sequences: 218,903 Dictionaries: 26 Vblocks: 2 x 512 MB Sections: 37
Genozip version: 13.0.5 github
Date compressed: 2021-12-03 10:31:26 ACDT
Command line: genozip --stats --best --multiseq ERR2708427.1.fastq.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 123.2 MB 72.7% 254.1 MB 47.3% 2.1X
SEQ 41.8 MB 24.6% 254.1 MB 47.3% 6.1X
DESC 4.6 MB 2.7% 14.0 MB 2.6% 3.1X
Other 470 B 0.0% 1.3 MB 0.2% 2794.5X
TXT_HEADER 348 B 0.0% - 0.0% 0.0X
LINE3 54 B 0.0% 14.0 MB 2.6% 271727.3X
GENOZIP vs BGZF 169.5 MB 100.0% 267.7 MB 100.0% 1.6X
GENOZIP vs TXT 169.5 MB 100.0% 537.5 MB 100.0% 3.2X
FASTQ - BGI data
FASTQ files (paired): V300016152A_L01_read_1.fq.gz V300016152A_L01_read_2.fq.gz
Reference: hs37d5.ref.genozip MD5=b0e641c998cc3eae6fa2f8726d98cddd genozip_version=12
Sequences: 850,258,934 Dictionaries: 38 Vblocks: 532 x 512 MB Sections: 9013
Read name style: BGI-R9/
Genozip version: 13.0.8 github
Date compressed: 2022-01-05 22:53:48 ACDT
Command line: genozip -e hs37d5.ref.genozip -tw2 -f --best V300016152A_L01_read_1.fq.gz V300016152A_L01_read_2.fq.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 43.8 GB 89.8% 118.8 GB 44.7% 2.7X
SEQ 4.9 GB 10.0% 118.8 GB 44.7% 24.3X
DESC 77.1 MB 0.2% 23.2 GB 8.7% 307.9X
Other 63.9 KB 0.0% 4.8 GB 1.8% 78018.5X
LINE3 21.3 KB 0.0% - 0.0% 0.0X
GENOZIP vs GZ 48.8 GB 100.0% 99.9 GB 100.0% 2.0X
GENOZIP vs TXT 48.8 GB 100.0% 265.5 GB 100.0% 5.4X
BAM - 30x Illumina NovaSeq + Dragen:
BAM file: <redacted>.bam
Reference: hs37d5.ref.genozip
Alignments: 636,660,181 Dictionaries: 161 Vblocks: 389 x 512 MB Sections: 17340
Sorting: Sorted by POS
Read name style: Illumina
Genozip version: 13.0.2 github
Date compressed: 2021-11-09 17:14:19 Cen. Australia Daylight Time
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 5.7 GB 57.2% 87.9 GB 45.3% 15.3X
QNAME 1.9 GB 19.3% 23.4 GB 12.1% 12.1X
SEQ 890.2 MB 8.7% 46.5 GB 24.0% 53.5X
PNEXT 441.8 MB 4.3% 2.4 GB 1.2% 5.5X
POS 211.0 MB 2.1% 2.4 GB 1.2% 11.5X
CIGAR 183.2 MB 1.8% 3.8 GB 1.9% 21.1X
FLAG 151.9 MB 1.5% 1.2 GB 0.6% 8.0X
XS:i 139.6 MB 1.4% 973.5 MB 0.5% 7.0X
AS:i 124.6 MB 1.2% 2.4 GB 1.2% 19.5X
TLEN 119.6 MB 1.2% 2.4 GB 1.2% 20.3X
XQ:i 70.4 MB 0.7% 580.0 MB 0.3% 8.2X
Other 41.7 MB 0.4% 10.1 GB 5.2% 248.6X
MAPQ 20.3 MB 0.2% 607.2 MB 0.3% 29.9X
SA:Z 7.8 MB 0.1% 31.2 MB 0.0% 4.0X
RNEXT 6.6 MB 0.1% 2.4 GB 1.2% 367.5X
RNAME 24.4 KB 0.0% 2.4 GB 1.2% 101926.8X
NM:i 12.6 KB 0.0% 2.4 GB 1.2% 196672.2X
TXT_HEADER 5.6 KB 0.0% 16.8 KB 0.0% 3.0X
BAM_BIN 43 B 0.0% 1.2 GB 0.6% 29612100.0X
RG:Z 42 B 0.0% 1.2 GB 0.6% 30317150.0X
GENOZIP vs BGZF 10.0 GB 100.0% 41.0 GB 100.0% 4.1X
GENOZIP vs TXT 10.0 GB 100.0% 194.0 GB 100.0% 19.4X
BAM - PacBio CLR (mapped)
BAM file: NA12878.pacbio.bwa-sw.20140202.bam
Reference: hs37d5.ref.genozip
Alignments: 25,968,256 Dictionaries: 163 Vblocks: 215 x 512 MB Sections: 9825
Sorting: Sorted by POS
Read name style: PacBio-Range
Genozip version: 13.0.5 github
Date compressed: 2021-11-30 21:05:14 ACDT
Command line: genozip --reference hs37d5.ref.genozip --best --stats NA12878.pacbio.bwa-sw.20140202.bam
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 19.3 GB 69.2% 41.1 GB 38.3% 2.1X
SEQ 3.7 GB 13.3% 20.6 GB 19.2% 5.6X
CIGAR 2.4 GB 8.6% 22.6 GB 21.1% 9.4X
SA:Z 2.3 GB 8.2% 19.1 GB 17.8% 8.4X
QNAME 103.6 MB 0.4% 1.9 GB 1.8% 18.7X
AS:i 32.0 MB 0.1% 38.0 MB 0.0% 1.2X
XS:i 31.1 MB 0.1% 29.2 MB 0.0% 0.9X
POS 24.5 MB 0.1% 99.1 MB 0.1% 4.0X
Other 11.6 MB 0.0% 520.0 MB 0.5% 44.9X
MAPQ 10.6 MB 0.0% 24.8 MB 0.0% 2.3X
FLAG 7.1 MB 0.0% 49.5 MB 0.0% 6.9X
PNEXT 51.7 KB 0.0% 99.1 MB 0.1% 1962.5X
NM:i 49.2 KB 0.0% 29.9 MB 0.0% 622.7X
RNAME 10.8 KB 0.0% 99.1 MB 0.1% 9369.7X
RNEXT 9.5 KB 0.0% 99.1 MB 0.1% 10686.5X
TXT_HEADER 4.0 KB 0.0% 19.7 KB 0.0% 5.0X
TLEN 83 B 0.0% 99.1 MB 0.1% 1251482.2X
RG:Z 56 B 0.0% 396.2 MB 0.4% 7419501.5X
PG:Z 55 B 0.0% 371.5 MB 0.3% 7082251.5X
BAM_BIN 43 B 0.0% 49.5 MB 0.0% 1207825.9X
GENOZIP vs BGZF 28.0 GB 100.0% 53.8 GB 100.0% 1.9X
GENOZIP vs TXT 28.0 GB 100.0% 107.3 GB 100.0% 3.8X
BAM - PacBio CCS (mapped)
BAM file: chm13.draft_v1.1.hifi_20k.wm_2.01.pri.bam
Reference: chm13.draft_v1.1.ref.genozip
Alignments: 5,575,318 Dictionaries: 164 Vblocks: 286 x 512 MB Sections: 11865
Sorting: Sorted by POS
Read name style: PacBio-Label
Genozip version: 13.0.5 conda
Date compressed: 2021-12-08 13:35:00 ACDT
Command line: genozip -ftw -e chm13.draft_v1.1.ref.genozip --best chm13.draft_v1.1.hifi_20k.wm_2.01.pri.bam
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 38.3 GB 98.9% 93.5 GB 65.5% 2.4X
CIGAR 273.3 MB 0.7% 1.4 GB 1.0% 5.4X
SEQ 75.4 MB 0.2% 46.8 GB 32.7% 635.7X
QNAME 16.7 MB 0.0% 188.1 MB 0.1% 11.2X
AS:i 9.4 MB 0.0% 10.6 MB 0.0% 1.1X
ms:i 9.0 MB 0.0% 10.6 MB 0.0% 1.2X
s1:i 8.2 MB 0.0% 10.6 MB 0.0% 1.3X
POS 7.4 MB 0.0% 21.3 MB 0.0% 2.9X
Other 5.9 MB 0.0% 196.8 MB 0.1% 33.1X
cm:i 5.9 MB 0.0% 10.6 MB 0.0% 1.8X
rl:i 5.4 MB 0.0% 6.9 MB 0.0% 1.3X
de:f 4.0 MB 0.0% 21.3 MB 0.0% 5.3X
s2:i 842.4 KB 0.0% 5.7 MB 0.0% 6.9X
FLAG 721.6 KB 0.0% 10.6 MB 0.0% 15.1X
SA:Z 330.1 KB 0.0% 596.4 KB 0.0% 1.8X
MD:Z 35.2 KB 0.0% 533.8 MB 0.4% 15524.7X
MAPQ 33.7 KB 0.0% 5.3 MB 0.0% 161.6X
PNEXT 32.5 KB 0.0% 21.3 MB 0.0% 670.5X
nn:i 13.2 KB 0.0% 5.3 MB 0.0% 412.3X
RNEXT 12.4 KB 0.0% 21.3 MB 0.0% 1753.8X
RNAME 12.1 KB 0.0% 21.3 MB 0.0% 1801.1X
TXT_HEADER 2.3 KB 0.0% 24.6 KB 0.0% 10.8X
zd:i 1.2 KB 0.0% 69 B 0.0% 0.1X
tp:A 233 B 0.0% 5.3 MB 0.0% 23928.4X
NM:i 85 B 0.0% 5.3 MB 0.0% 65785.6X
TLEN 83 B 0.0% 21.3 MB 0.0% 268690.0X
BAM_BIN 43 B 0.0% 10.6 MB 0.0% 259317.1X
GENOZIP vs BGZF 38.7 GB 100.0% 73.8 GB 100.0% 1.9X
GENOZIP vs TXT 38.7 GB 100.0% 142.8 GB 100.0% 3.7X
BAM - Nanopore (mapped)
BAM file: chm13.draft_v1.1.ont_guppy_3.6.0.wm_2.01.pri.bam
Reference: chm13.draft_v1.1.ref.genozip
Alignments: 13,364,876 Dictionaries: 168 Vblocks: 1321 x 512 MB Sections: 65852
Sorting: Sorted by POS
Read name style: Nanopore
Genozip version: 13.0.6 github
Date compressed: 2021-12-08 02:36:21 ACDT
Command line: genozip --best -wtf -e chm13.draft_v1.1.ref.genozip chm13.draft_v1.1.ont_guppy_3.6.0.wm_2.01.pri.bam
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 186.1 GB 88.9% 351.6 GB 53.3% 1.9X
CIGAR 11.8 GB 5.6% 84.2 GB 12.8% 7.2X
SEQ 11.0 GB 5.3% 175.9 GB 26.6% 15.9X
QNAME 214.8 MB 0.1% 484.3 MB 0.1% 2.3X
MD:Z 39.6 MB 0.0% 46.7 GB 7.1% 1208.4X
AS:i 27.8 MB 0.0% 30.6 MB 0.0% 1.1X
SA:Z 26.9 MB 0.0% 154.8 MB 0.0% 5.8X
ms:i 25.0 MB 0.0% 30.6 MB 0.0% 1.2X
s1:i 21.9 MB 0.0% 23.1 MB 0.0% 1.1X
Other 20.9 MB 0.0% 475.1 MB 0.1% 22.8X
de:f 17.4 MB 0.0% 51.0 MB 0.0% 2.9X
cm:i 16.3 MB 0.0% 18.6 MB 0.0% 1.1X
POS 15.3 MB 0.0% 51.0 MB 0.0% 3.3X
CG:B:I 14.3 MB 0.0% 118.9 MB 0.0% 8.3X
rl:i 6.7 MB 0.0% 13.6 MB 0.0% 2.0X
s2:i 3.7 MB 0.0% 13.4 MB 0.0% 3.6X
FLAG 2.1 MB 0.0% 25.5 MB 0.0% 12.3X
MAPQ 1.6 MB 0.0% 12.7 MB 0.0% 8.0X
PNEXT 167.9 KB 0.0% 51.0 MB 0.0% 311.0X
zd:i 126.6 KB 0.0% 109.7 KB 0.0% 0.9X
nn:i 59.4 KB 0.0% 12.7 MB 0.0% 219.6X
RNEXT 56.9 KB 0.0% 51.0 MB 0.0% 917.7X
RNAME 52.6 KB 0.0% 51.0 MB 0.0% 993.3X
NM:i 39.2 KB 0.0% 21.8 MB 0.0% 569.9X
tp:A 28.1 KB 0.0% 12.7 MB 0.0% 464.4X
TXT_HEADER 1.8 KB 0.0% 12.0 KB 0.0% 6.8X
TLEN 83 B 0.0% 51.0 MB 0.0% 644090.4X
BAM_BIN 43 B 0.0% 25.5 MB 0.0% 621622.1X
GENOZIP vs BGZF 209.3 GB 100.0% 384.1 GB 100.0% 1.8X
GENOZIP vs TXT 209.3 GB 100.0% 660.1 GB 100.0% 3.2X
CRAM - Illumina NovaSeq + bwa mem
SAM file: NA12878.final.cram
Reference: GRCh38_full_analysis_set_plus_decoy_hla.ref.genozip
Alignments: 768,580,569 Dictionaries: 160 Vblocks: 749 x 512 MB Sections: 44749
Sorting: Sorted by POS
Read name style: Illumina
Genozip version: 13.0.2 conda
Date compressed: 2021-11-09 17:32:34 ACDT
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
QUAL 2.7 GB 27.7% 108.1 GB 28.9% 39.9X
QNAME 2.4 GB 24.7% 27.5 GB 7.4% 11.4X
XA:Z 1.4 GB 14.8% 13.7 GB 3.7% 9.5X
SEQ 925.9 MB 9.3% 108.1 GB 28.9% 119.5X
PNEXT 630.8 MB 6.3% 6.6 GB 1.8% 10.7X
XS:i 305.0 MB 3.1% 2.1 GB 0.6% 7.2X
POS 275.7 MB 2.8% 6.6 GB 1.8% 24.4X
RG:Z 275.0 MB 2.8% 29.3 GB 7.8% 109.3X
FLAG 213.7 MB 2.1% 2.6 GB 0.7% 12.6X
AS:i 129.6 MB 1.3% 2.8 GB 0.8% 22.4X
SA:Z 115.3 MB 1.2% 838.7 MB 0.2% 7.3X
MAPQ 112.9 MB 1.1% 2.1 GB 0.6% 19.1X
MC:Z 106.3 MB 1.1% 3.8 GB 1.0% 36.5X
CIGAR 91.8 MB 0.9% 3.8 GB 1.0% 42.2X
MQ:i 37.0 MB 0.4% 2.1 GB 0.6% 57.5X
RNEXT 20.6 MB 0.2% 1.5 GB 0.4% 76.5X
Other 17.6 MB 0.2% 29.0 GB 7.8% 1692.4X
TLEN 14.0 MB 0.1% 3.2 GB 0.9% 233.7X
pa:f 6.9 MB 0.1% 38.5 MB 0.0% 5.6X
MD:Z 1.2 MB 0.0% 4.0 GB 1.1% 3464.2X
RNAME 374.0 KB 0.0% 4.1 GB 1.1% 11515.0X
TXT_HEADER 72.5 KB 0.0% 626.9 KB 0.0% 8.6X
NM:i 66.8 KB 0.0% 1.4 GB 0.4% 22624.0X
Reference 112 B 0.0% - 0.0% 0.0X
PG:Z 55 B 0.0% 10.7 GB 2.9% 209612880.0X
BAM_BIN 43 B 0.0% - 0.0% 0.0X
TOTAL 9.8 GB 100.0% 374.2 GB 100.0% 38.3X
VCF - 3202 samples from the 1000 Genomes Project
VCF file: 20201028_CCDG_14151_B01_GRM_WGS_2020-08-05_chr22.recalibrated_variants.vcf.gz
Samples: 3202 Variants: 1,927,372 Dictionaries: 401 Vblocks: 351 x 512 MB Sections: 158051
Genozip version: 13.0.3 github
Date compressed: 2021-11-14 08:56:28 ACDT
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
FORMAT/PL 5.0 GB 64.3% 59.4 GB 33.9% 11.8X
FORMAT/AD 2.4 GB 30.9% 24.7 GB 14.1% 10.2X
FORMAT/GT 67.2 MB 0.8% 17.2 GB 9.8% 262.8X
FORMAT/GQ 65.3 MB 0.8% 11.2 GB 6.4% 176.0X
FORMAT/PID 63.5 MB 0.8% 3.2 GB 1.8% 51.6X
FORMAT/PGT 38.4 MB 0.5% 2.3 GB 1.3% 60.1X
FORMAT/DP 19.6 MB 0.2% 11.4 GB 6.5% 593.2X
FORMAT/AB 14.9 MB 0.2% 5.7 GB 3.2% 388.8X
INFO/AC_Het_EUR_unre 5.9 MB 0.1% 26.9 MB 0.0% 4.6X
QUAL 5.1 MB 0.1% 13.7 MB 0.0% 2.7X
INFO/DP 4.4 MB 0.1% 10.5 MB 0.0% 2.4X
INFO/AF_AMR_unrel 3.4 MB 0.0% 20.4 MB 0.0% 6.0X
INFO/VQSLOD 3.3 MB 0.0% 9.6 MB 0.0% 2.9X
INFO/FS 3.0 MB 0.0% 7.3 MB 0.0% 2.5X
INFO/AF 2.9 MB 0.0% 21.9 MB 0.0% 7.6X
INFO/MQRankSum 2.8 MB 0.0% 9.3 MB 0.0% 3.3X
INFO/SOR 2.8 MB 0.0% 9.0 MB 0.0% 3.2X
INFO/BaseQRankSum 2.8 MB 0.0% 9.2 MB 0.0% 3.4X
INFO/QD 2.7 MB 0.0% 8.5 MB 0.0% 3.1X
INFO/ReadPosRankSum 2.7 MB 0.0% 9.0 MB 0.0% 3.3X
INFO/AF_EUR_unrel 2.7 MB 0.0% 16.9 MB 0.0% 6.2X
INFO/ClippingRankSum 2.7 MB 0.0% 9.3 MB 0.0% 3.4X
INFO/AC_AMR_unrel 2.3 MB 0.0% 5.8 MB 0.0% 2.5X
INFO/MLEAF 2.3 MB 0.0% 17.3 MB 0.0% 7.7X
INFO/AF_AFR 2.2 MB 0.0% 11.9 MB 0.0% 5.4X
INFO/ExcHet 2.2 MB 0.0% 10.8 MB 0.0% 4.9X
INFO/AC_Het_AFR 2.1 MB 0.0% 5.7 MB 0.0% 2.8X
INFO/InbreedingCoeff 2.0 MB 0.0% 10.8 MB 0.0% 5.5X
INFO/ExcHet_AFR 1.9 MB 0.0% 7.8 MB 0.0% 4.0X
REF+ALT 1.9 MB 0.0% 12.4 MB 0.0% 6.4X
INFO/MLEAC 1.9 MB 0.0% 3.5 MB 0.0% 1.8X
INFO/HWE 1.9 MB 0.0% 6.2 MB 0.0% 3.2X
INFO/AC_EUR_unrel 1.9 MB 0.0% 5.6 MB 0.0% 2.9X
INFO/AC_Het 1.9 MB 0.0% 3.4 MB 0.0% 1.8X
INFO/AF_SAS 1.6 MB 0.0% 9.2 MB 0.0% 5.6X
INFO/AF_AMR 1.6 MB 0.0% 8.9 MB 0.0% 5.5X
INFO/AC_AFR 1.6 MB 0.0% 3.1 MB 0.0% 1.9X
INFO/AF_EUR 1.6 MB 0.0% 8.6 MB 0.0% 5.4X
INFO/AF_SAS_unrel 1.6 MB 0.0% 8.8 MB 0.0% 5.6X
INFO/AC_Het_SAS 1.5 MB 0.0% 5.4 MB 0.0% 3.5X
INFO/AF_EAS 1.5 MB 0.0% 8.5 MB 0.0% 5.6X
INFO/AC_Het_AMR 1.5 MB 0.0% 5.3 MB 0.0% 3.5X
POS 1.5 MB 0.0% 16.5 MB 0.0% 11.2X
INFO/AC_Het_EUR 1.5 MB 0.0% 5.4 MB 0.0% 3.7X
INFO/HWE_AFR 1.4 MB 0.0% 5.0 MB 0.0% 3.5X
INFO/AC_Het_EAS 1.4 MB 0.0% 5.3 MB 0.0% 3.8X
INFO/ExcHet_AMR 1.4 MB 0.0% 6.2 MB 0.0% 4.4X
INFO/ExcHet_SAS 1.4 MB 0.0% 5.9 MB 0.0% 4.3X
INFO/MQ 1.4 MB 0.0% 5.8 MB 0.0% 4.3X
INFO/ExcHet_EUR 1.3 MB 0.0% 5.7 MB 0.0% 4.2X
INFO/ExcHet_EAS 1.3 MB 0.0% 5.4 MB 0.0% 4.3X
INFO/AC_SAS 1.2 MB 0.0% 2.8 MB 0.0% 2.3X
INFO/AC_AMR 1.2 MB 0.0% 2.8 MB 0.0% 2.3X
INFO/AC_EUR 1.2 MB 0.0% 2.8 MB 0.0% 2.4X
INFO/AC_SAS_unrel 1.2 MB 0.0% 2.8 MB 0.0% 2.4X
INFO/AC_EAS 1.1 MB 0.0% 2.8 MB 0.0% 2.5X
INFO/HWE_SAS 1.1 MB 0.0% 4.2 MB 0.0% 4.0X
INFO/HWE_AMR 1.0 MB 0.0% 4.1 MB 0.0% 4.0X
INFO/HWE_EUR 1.0 MB 0.0% 4.1 MB 0.0% 4.0X
INFO/HWE_EAS 981.2 KB 0.0% 4.0 MB 0.0% 4.1X
INFO/AC_Hom 936.7 KB 0.0% 2.8 MB 0.0% 3.1X
INFO/ME 926.4 KB 0.0% 4.5 MB 0.0% 4.9X
INFO/AC 778.4 KB 0.0% 3.5 MB 0.0% 4.6X
INFO/AN_AMR_unrel 537.4 KB 0.0% 12.8 MB 0.0% 24.5X
INFO 479.4 KB 0.0% 1.6 GB 0.9% 3600.3X
INFO/AN_EUR_unrel 472.6 KB 0.0% 14.4 MB 0.0% 31.2X
INFO/AN 457.6 KB 0.0% 7.4 MB 0.0% 16.4X
Other 391.4 KB 0.0% 38.1 GB 21.7% 102014.1X
FORMAT 347.0 KB 0.0% 37.9 MB 0.0% 111.8X
INFO/culprit 340.1 KB 0.0% 5.5 MB 0.0% 16.7X
INFO/AN_AFR 337.9 KB 0.0% 7.3 MB 0.0% 22.2X
INFO/AN_EUR 285.7 KB 0.0% 7.3 MB 0.0% 26.2X
INFO/AN_SAS 283.2 KB 0.0% 7.3 MB 0.0% 26.4X
INFO/AN_EAS 273.6 KB 0.0% 7.3 MB 0.0% 27.3X
INFO/AN_AMR 272.8 KB 0.0% 5.5 MB 0.0% 20.7X
INFO/AN_SAS_unrel 266.6 KB 0.0% 5.5 MB 0.0% 21.2X
FILTER 147.0 KB 0.0% 15.0 MB 0.0% 104.6X
INFO/NEGATIVE_TRAIN_ 14.1 KB 0.0% - 0.0% 0.0X
TXT_HEADER 13.2 KB 0.0% 201.7 KB 0.0% 15.2X
INFO/POSITIVE_TRAIN_ 12.2 KB 0.0% - 0.0% 0.0X
COORDS 536 B 0.0% - 0.0% 0.0X
CHROM 139 B 0.0% 11.0 MB 0.0% 83195.9X
ID 42 B 0.0% 3.7 MB 0.0% 91779.6X
INFO/MQ0 42 B 0.0% 1.8 MB 0.0% 45889.8X
GENOZIP vs BGZF 7.8 GB 100.0% 26.0 GB 100.0% 3.3X
GENOZIP vs TXT 7.8 GB 100.0% 175.3 GB 100.0% 22.4X
VCF - 1135 Arabidopsis Thaliana samples
VCF file: 1001genomes_snp-short-indel_with_tair10_only_ACGTN.vcf.gz
Samples: 1135 Variants: 119,146,348 Dictionaries: 190 Vblocks: 2398 x 512 MB Sections: 56957
Genozip version: 13.0.5 github
Date compressed: 2021-11-22 11:28:13 ACDT
Command line: genozip --stats --best 1001genomes_snp-short-indel_with_tair10_only_ACGTN.vcf.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
FORMAT/DP 22.6 GB 71.6% 206.5 GB 17.2% 9.1X
FORMAT/GQ 8.7 GB 27.5% 231.7 GB 19.3% 26.6X
FORMAT/GT 237.1 MB 0.7% 377.8 GB 31.5% 1631.6X
REF+ALT 41.4 MB 0.1% 460.5 MB 0.0% 11.1X
QUAL 928.5 KB 0.0% 340.9 MB 0.0% 376.0X
Other 296.1 KB 0.0% 377.8 GB 31.5% 1337972.4X
POS 236.6 KB 0.0% 969.7 MB 0.1% 4197.5X
CHROM 74.6 KB 0.0% 227.3 MB 0.0% 3119.3X
TXT_HEADER 1.5 KB 0.0% 6.0 KB 0.0% 3.9X
COORDS 547 B 0.0% - 0.0% 0.0X
INFO 76 B 0.0% 454.5 MB 0.0% 6270860.5X
FORMAT 51 B 0.0% 1022.6 MB 0.1% 21025826.0X
INFO/DP 49 B 0.0% 545.3 MB 0.0% 11669053.0X
FILTER 45 B 0.0% 568.1 MB 0.0% 13238482.0X
ID 42 B 0.0% 227.3 MB 0.0% 5673636.0X
GENOZIP vs BGZF 31.6 GB 100.0% 132.4 GB 100.0% 4.2X
GENOZIP vs TXT 31.6 GB 100.0% 1.2 TB 100.0% 37.9X
VCF - 3K Rice Genome
VCF file: IRIS_313-10000.snp.vcf.gz
Samples: 1 Variants: 409,606,670 Dictionaries: 302 Vblocks: 52 x 512 MB Sections: 3288
Genozip version: 13.0.4 github
Date compressed: 2021-11-20 20:51:00 ACDT
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
REF+ALT 93.3 MB 29.6% 1.5 GB 5.9% 16.7X
QUAL 70.0 MB 22.2% 2.0 GB 7.8% 29.7X
INFO/MQ 68.2 MB 21.6% 1.7 GB 6.4% 25.0X
INFO/DP 52.3 MB 16.6% 593.1 MB 2.2% 11.3X
INFO/MQ0 6.6 MB 2.1% 360.3 MB 1.4% 54.5X
INFO 3.4 MB 1.1% 5.8 GB 22.4% 1757.9X
FORMAT/DP 2.7 MB 0.8% 561.5 MB 2.1% 211.5X
FORMAT/PL 2.6 MB 0.8% 11.2 MB 0.0% 4.3X
FORMAT/GT 2.6 MB 0.8% 1.1 GB 4.4% 454.9X
Other 2.6 MB 0.8% 716.6 MB 2.7% 280.6X
FORMAT 2.5 MB 0.8% 2.1 GB 8.1% 848.9X
INFO/QD 2.1 MB 0.7% 6.8 MB 0.0% 3.3X
FORMAT/AD 1.1 MB 0.3% 5.2 MB 0.0% 4.7X
FILTER 902.5 KB 0.3% 785.2 MB 3.0% 890.9X
FORMAT/GQ 811.5 KB 0.3% 2.7 MB 0.0% 3.4X
POS 715.0 KB 0.2% 3.2 GB 12.2% 4627.1X
INFO/MQRankSum 647.9 KB 0.2% 2.3 MB 0.0% 3.6X
INFO/ReadPosRankSum 643.2 KB 0.2% 2.2 MB 0.0% 3.5X
INFO/BaseQRankSum 638.8 KB 0.2% 2.2 MB 0.0% 3.5X
INFO/HaplotypeScore 443.5 KB 0.1% 7.7 MB 0.0% 17.8X
INFO/FS 373.2 KB 0.1% 7.2 MB 0.0% 19.7X
CHROM 137.7 KB 0.0% 4.4 GB 17.1% 33717.5X
INFO/MLEAF 82.6 KB 0.0% 6.1 MB 0.0% 75.2X
INFO/MLEAC 82.6 KB 0.0% 1.4 MB 0.0% 17.7X
INFO/AF 82.1 KB 0.0% 6.1 MB 0.0% 75.6X
INFO/RPA 77.6 KB 0.0% 317.9 KB 0.0% 4.1X
INFO/RU 64.3 KB 0.0% 138.0 KB 0.0% 2.1X
TXT_HEADER 46.7 KB 0.0% 546.0 KB 0.0% 11.7X
INFO/Dels 35.0 KB 0.0% 5.1 MB 0.0% 149.8X
INFO/AC 4.7 KB 0.0% 1.4 MB 0.0% 313.4X
INFO/STR 2.1 KB 0.0% - 0.0% 0.0X
COORDS 547 B 0.0% - 0.0% 0.0X
INFO/AN 83 B 0.0% 321.7 MB 1.2% 4064608.5X
ID 42 B 0.0% 781.3 MB 2.9% 19505078.0X
GENOZIP vs BGZF 315.5 MB 100.0% 1.9 GB 100.0% 6.2X
GENOZIP vs TXT 315.5 MB 100.0% 26.0 GB 100.0% 84.3X
FASTA - Covid-19 multi-FASTA
FASTA file: coronavirus.unwrapped.fasta.gz
Lines: 89,836 Dictionaries: 11 Vblocks: 3 x 512 MB Sections: 32
Sequence type: Nucleotide bases
Genozip version: 13.0.5 github
Date compressed: 2021-12-03 11:25:06 ACDT
Command line: genozip --best --stats --multiseq coronavirus.unwrapped.fasta.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
NONREF 1.4 MB 92.6% 1.2 GB 100.0% 904.8X
Other 95.3 KB 6.2% 87.7 KB 0.0% 0.9X
DESC 18.1 KB 1.2% 526.3 KB 0.0% 29.1X
GENOZIP vs BGZF 1.5 MB 100.0% 254.9 MB 100.0% 170.0X
GENOZIP vs TXT 1.5 MB 100.0% 1.2 GB 100.0% 838.4X
GFF3 - Gene annotation
GFF3 file: chm13.draft_v1.0.gene_annotation.v4.gff3.gz
Sequences: 3,873,663 Dictionaries: 79 Vblocks: 8 x 512 MB Sections: 562
Genozip version: 13.0.5 conda
Date compressed: 2021-12-08 12:07:18 ACDT
Command line: genozip -ft --best --stats chm13.draft_v1.0.gene_annotation.v4.gff3.gz
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
ID 4.5 MB 13.9% 78.6 MB 2.1% 17.5X
END 3.0 MB 9.1% 34.0 MB 0.9% 11.5X
alignment_id 2.0 MB 6.1% 69.1 MB 1.8% 35.0X
source_transcript 1.9 MB 5.9% 60.8 MB 1.6% 31.9X
source_gene_common_n 1.9 MB 5.8% 56.2 MB 1.5% 29.9X
START 1.7 MB 5.2% 34.0 MB 0.9% 20.3X
transcript_name 1.7 MB 5.1% 35.9 MB 0.9% 21.7X
Parent 1.6 MB 4.9% 50.9 MB 1.3% 32.1X
havana_transcript 1.5 MB 4.7% 64.2 MB 1.7% 42.5X
transcript_id 1.3 MB 4.1% 50.9 MB 1.3% 38.6X
intron_annotation_su 1.2 MB 3.8% 101.0 MB 2.7% 83.3X
exon_anotation_suppo 1.0 MB 3.2% 108.3 MB 2.8% 104.2X
protein_id 997.4 KB 3.0% 45.0 MB 1.2% 46.2X
adj_stop 825.9 KB 2.5% 22.3 MB 0.6% 27.6X
ATTRS 818.0 KB 2.5% 2.1 GB 56.8% 2711.0X
adj_start 804.7 KB 2.4% 22.3 MB 0.6% 28.3X
tag 689.3 KB 2.1% 84.8 MB 2.2% 125.9X
transcript_support_l 569.0 KB 1.7% 3.1 MB 0.1% 5.7X
transcript_biotype 420.6 KB 1.3% 53.9 MB 1.4% 131.2X
Name 394.6 KB 1.2% 21.8 MB 0.6% 56.6X
TYPE 386.3 KB 1.2% 22.4 MB 0.6% 59.4X
gene_name 326.5 KB 1.0% 51.3 MB 1.3% 160.9X
PHASE 321.0 KB 1.0% 7.4 MB 0.2% 23.6X
SCORE 315.6 KB 1.0% 8.1 MB 0.2% 26.2X
source_gene 293.2 KB 0.9% 65.8 MB 1.7% 229.7X
ccdsid 258.3 KB 0.8% 14.6 MB 0.4% 57.9X
havana_gene 241.3 KB 0.7% 71.0 MB 1.9% 301.3X
proper_orf 205.7 KB 0.6% 14.9 MB 0.4% 74.4X
valid_stop 187.7 KB 0.6% 14.9 MB 0.4% 81.3X
level 176.8 KB 0.5% 3.5 MB 0.1% 20.4X
valid_start 170.5 KB 0.5% 14.9 MB 0.4% 89.2X
hgnc_id 164.9 KB 0.5% 32.1 MB 0.8% 199.6X
gene_id 129.5 KB 0.4% 51.7 MB 1.4% 408.8X
frameshift 127.2 KB 0.4% 11.1 MB 0.3% 89.4X
unfiltered_paralogy 115.3 KB 0.3% 11.7 MB 0.3% 103.9X
paralogy 76.8 KB 0.2% 11.1 MB 0.3% 147.7X
transcript_class 76.4 KB 0.2% 30.6 MB 0.8% 409.8X
gene_biotype 54.5 KB 0.2% 49.9 MB 1.3% 937.7X
SEQID 45.4 KB 0.1% 20.2 MB 0.5% 456.6X
STRAND 33.0 KB 0.1% 7.4 MB 0.2% 229.2X
transcript_modes 32.5 KB 0.1% 29.3 MB 0.8% 921.5X
rna_support 31.0 KB 0.1% 10.3 MB 0.3% 340.7X
collapsed_gene_names 22.2 KB 0.1% 15.1 MB 0.4% 695.0X
collapsed_gene_ids 20.8 KB 0.1% 18.7 MB 0.5% 917.8X
gene_alternate_conti 18.2 KB 0.1% 1.6 MB 0.0% 90.2X
alternative_source_t 5.7 KB 0.0% 11.1 MB 0.3% 1982.3X
ont 4.6 KB 0.0% 679.7 KB 0.0% 147.0X
Other 1.7 KB 0.0% - 0.0% 0.0X
possible_split_gene_ 1.3 KB 0.0% 12.5 KB 0.0% 9.5X
novel_5p_cap 1.0 KB 0.0% 394.9 KB 0.0% 383.7X
TXT_HEADER 364 B 0.0% 16 B 0.0% 0.0X
COMMENT 328 B 0.0% - 0.0% 0.0X
SOURCE 160 B 0.0% 14.8 MB 0.4% 97251.2X
extra_paralog 159 B 0.0% 18.5 MB 0.5% 121710.3X
novel_poly_a 130 B 0.0% 390.6 KB 0.0% 3076.8X
reference_support 45 B 0.0% 13.6 MB 0.4% 317191.9X
GENOZIP vs GZ 32.3 MB 100.0% 91.8 MB 100.0% 2.8X
GENOZIP vs TXT 32.3 MB 100.0% 3.7 GB 100.0% 117.9X
23andMe - Consumer DNA test “raw data”
23ANDME file: genome_<redacted>.txt
SNPs: 960,613 Dictionaries: 7 Vblocks: 2 x 16 MB Sections: 27
Genozip version: 13.0.2 github
Date compressed: 2021-11-09 18:05:24 Cen. Australia Daylight Time
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
ID 2.3 MB 55.2% 9.3 MB 39.5% 4.1X
POS 1.5 MB 37.1% 8.4 MB 35.8% 5.5X
GENOTYPE 327.5 KB 7.7% 2.7 MB 11.5% 8.5X
CHROM 1.9 KB 0.0% 2.2 MB 9.4% 1200.4X
TXT_HEADER 931 B 0.0% 940 B 0.0% 1.0X
Other 804 B 0.0% 938.1 KB 3.9% 1194.8X
TOTAL 4.2 MB 100.0% 23.6 MB 100.0% 5.7X
Illumina s.locs file
LOCS file: s.locs
Clusters: 4,091,904 Dictionaries: 3 Vblocks: 1 x 512 MB Sections: 9
Genozip version: 13.0.5
Date compressed: 2021-11-28 16:51:17 Cen. Australia Daylight Time
Command line: genozip --best --stats s.locs
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
X 3.0 KB 79.9% 15.6 MB 50.0% 5410.8X
TXT_HEADER 360 B 9.5% 12 B 0.0% 0.0X
Y 239 B 6.3% 15.6 MB 50.0% 68483.8X
Other 162 B 4.3% - 0.0% 0.0X
TOTAL 3.7 KB 100.0% 31.2 MB 100.0% 8646.4X
Note: ZIP total file size excludes overhead of 2.2 KB
Illumina locs file (for example: s_1_1101.locs)
LOCS file: s_1_1101.locs
Clusters: 812,166 Dictionaries: 3 Vblocks: 1 x 512 MB Sections: 9
Genozip version: 13.0.5
Date compressed: 2021-11-28 16:57:58 Cen. Australia Daylight Time
Command line: genozip --best --stats s_1_1101.locs
Sections (sorted by % of genozip file):
NAME GENOZIP % TXT % RATIO
X 2.6 MB 78.5% 3.1 MB 50.0% 1.2X
Y 720.1 KB 21.5% 3.1 MB 50.0% 4.4X
TXT_HEADER 360 B 0.0% 12 B 0.0% 0.0X
Other 162 B 0.0% - 0.0% 0.0X
TOTAL 3.3 MB 100.0% 6.2 MB 100.0% 1.9X
