Schema for dbVar - Structural Variations in dbVar |
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Database: dm6 Primary Table: dbvar_nstd134_call
VCF File: /gbdb/dm6/bbi/vcf/nstd134.submitted.variant_call.vcf.gz
Format description: The fields of a Variant Call Format data line
See the Variant Call Format specification for more details
| field | description |
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| chrom | An identifier from the reference genome | | pos | The reference position, with the 1st base having position 1 | | id | Semi-colon separated list of unique identifiers where available | | ref | Reference base(s) | | alt | Comma separated list of alternate non-reference alleles called on at least one of the samples | | qual | Phred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong) | | filter | PASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail | | info | Additional information encoded as a semicolon-separated series of short keys with optional comma-separated values | | format | If genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT | | genotypes | If genotype columns are specified in header, a tab-separated set of genotype column values; each value is a colon-separated list of values corresponding to keys in the format column |
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Sample Rows
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| chrom | pos | id | ref | alt | qual | filter | info |
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| chr2L | 86452 | nssv13657626 | A | | . | . | DBVARID;CALLID=chr2L_hc_tsxwm_alt_1;SVTYPE=INS;EXPERIMENT=1;SAMPLESET=1;END=86452;REGION=nsv2781011;AC=8;AF=0.018;AN=444 |
| chr2L | 130271 | nssv13657262 | C | | . | . | DBVARID;CALLID=chr2L_CNV_chr2L_130271_134470_alt_1;SVTYPE=DUP;EXPERIMENT=1;SAMPLESET=1;END=134469;REGION=nsv2780755;AC=90;AF=0.2 ... |
| chr2L | 263377 | nssv13657438 | G | | . | . | DBVARID;CALLID=chr2L_hc_injed_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=263445;REGION=nsv2781235;AC=170;AF=0.383;AN=444 |
| chr2L | 285506 | nssv13657675 | G | | . | . | DBVARID;CALLID=chr2L_hc_woiyg_alt_1;SVTYPE=INS;EXPERIMENT=1;SAMPLESET=1;END=285506;REGION=nsv2781297;AC=1;AF=0.002252;AN=444 |
| chr2L | 429368 | nssv13657282 | C | | . | . | DBVARID;CALLID=chr2L_hc_aezkh_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=429419;REGION=nsv2781690;AC=124;AF=0.279;AN=444 |
| chr2L | 602308 | nssv13657624 | T | | . | . | DBVARID;CALLID=chr2L_hc_tnyhg_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=602362;REGION=nsv2781053;AC=56;AF=0.126;AN=444 |
| chr2L | 609345 | nssv13657429 | T | | . | . | DBVARID;CALLID=chr2L_hc_iaujd_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=609408;REGION=nsv2781000;AC=67;AF=0.151;AN=444 |
| chr2L | 666211 | nssv13657616 | G | | . | . | DBVARID;CALLID=chr2L_hc_tdwxu_alt_1;SVTYPE=INS;EXPERIMENT=1;SAMPLESET=1;END=666211;REGION=nsv2781423;AC=68;AF=0.153;AN=444 |
| chr2L | 795312 | nssv13657500 | G | | . | . | DBVARID;CALLID=chr2L_hc_msajw_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=795369;REGION=nsv2779663;AC=95;AF=0.214;AN=444 |
| chr2L | 811082 | nssv13657714 | T | | . | . | DBVARID;CALLID=chr2L_hc_yztgb_alt_1;SVTYPE=DEL;EXPERIMENT=1;SAMPLESET=1;END=811203;REGION=nsv2780795;AC=1;AF=0.002252;AN=444 |
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dbVar (dbvar) Track Description
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Description
These tracks show the locations of large structural variations in the D. melanogaster genome from the NCBI dbVar database. The datasets were obtained from the NCBI FTP site, and they include the results from the following studies:
| Accession | Manuscript |
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| nstd25 |
Dopman EB, Hartl DL. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19920-5. |
| nstd26 |
Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 2008 Jun 20;320(5883):1629-31. |
| estd205 |
Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Res. 2013 Mar;23(3):568-79. |
| nstd134 |
Gilks WP, Pennell TM, Flis I, Webster MT, Morrow EH. Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample. Version 3. F1000Res. 2016 Nov 7 [revised 2016 Dec 22];5:2644. |
References
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41.
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