gnomad-structural-variants-data_description

Bed Example

The bed file was obtained from original source for GRCh37

#chrom  start   end name    svtype  ALGORITHMS  BOTHSIDES_SUPPORT   CHR2    CPX_INTERVALS   CPX_TYPE    END2    ENDEVIDENCE HIGH_SR_BACKGROUND  PCRPLUS_DEPLETED    PESR_GT_OVERDISPERSION  POS2    PROTEIN_CODING__COPY_GAIN   PROTEIN_CODING__DUP_LOF PROTEIN_CODING__DUP_PARTIAL PROTEIN_CODING__INTERGENIC  PROTEIN_CODING__INTRONIC    PROTEIN_CODING__INV_SPAN    PROTEIN_CODING__LOF PROTEIN_CODING__MSV_EXON_OVR    PROTEIN_CODING__NEAREST_TSS PROTEIN_CODING__PROMOTER    PROTEIN_CODING__UTR SOURCE  STRANDS SVLEN   SVTYPE  UNRESOLVED_TYPE UNSTABLE_AF_PCRPLUS VARIABLE_ACROSS_BATCHES AN  AC  AF  N_BI_GENOS  N_HOMREF    N_HET   N_HOMALT    FREQ_HOMREF FREQ_HET    FREQ_HOMALT MALE_AN MALE_AC MALE_AF MALE_N_BI_GENOS MALE_N_HOMREF   MALE_N_HET  MALE_N_HOMALT   MALE_FREQ_HOMREF    MALE_FREQ_HET   MALE_FREQ_HOMALT    MALE_N_HEMIREF  MALE_N_HEMIALT  MALE_FREQ_HEMIREF   MALE_FREQ_HEMIALT   PAR FEMALE_AN   FEMALE_AC   FEMALE_AF   FEMALE_N_BI_GENOS   FEMALE_N_HOMREF FEMALE_N_HET    FEMALE_N_HOMALT FEMALE_FREQ_HOMREF  FEMALE_FREQ_HET FEMALE_FREQ_HOMALT  POPMAX_AF   AFR_AN  AFR_AC  AFR_AF  AFR_N_BI_GENOS  AFR_N_HOMREF    AFR_N_HET   AFR_N_HOMALT    AFR_FREQ_HOMREF AFR_FREQ_HEAFR_FREQ_HOMALT  AFR_MALE_AN AFR_MALE_AC AFR_MALE_AF AFR_MALE_N_BI_GENOS AFR_MALE_N_HOMREF   AFR_MALE_N_HET  AFR_MALE_N_HOMALT   AFR_MALE_FREQ_HOMREF    AFR_MALE_FREQ_HET   AFR_MALE_FREQ_HOMALT    AFR_MALE_N_HEMIREF  AFR_MALE_N_HEMIALT  AFR_MALE_FREQ_HEMIREF   AFR_MALE_FREQ_HEMIALT   AFR_FEMALE_AN   AFR_FEMALE_AC   AFR_FEMALE_AF   AFR_FEMALE_N_BI_GENOS   AFR_FEMALE_N_HOMREF AFR_FEMALE_N_HET    AFR_FEMALE_N_HOMALT AFR_FEMALE_FREQ_HOMREF  AFR_FEMALE_FREQ_HET AFR_FEMALE_FREQ_HOMALT  AMR_AN  AMR_AC  AMR_AF  AMR_N_BI_GENOS  AMR_N_HOMREF    AMR_N_HET   AMR_N_HOMALT    AMR_FREQ_HOMREF AMR_FREQ_HET    AMR_FREQ_HOMALT AMR_MALE_AN AMR_MALE_AC AMR_MALE_AF AMR_MALE_N_BI_GENOS AMR_MALE_N_HOMREF   AMR_MALE_N_HET  AMR_MALE_N_HOMALT   AMR_MALE_FREQ_HOMREF    AMR_MALE_FREQ_HET   AMR_MALE_FREQ_HOMALT    AMR_MALE_N_HEMIREF  AMR_MALE_N_HEMIALT  AMR_MALE_FREQ_HEMIREF   AMR_MALE_FREQ_HEMIALT   AMR_FEMALE_AN   AMR_FEMALE_AC   AMR_FEMALE_AF   AMR_FEMALE_N_BI_GENOS   AMR_FEMALE_N_HOMREF AMR_FEMALE_N_HET    AMR_FEMALE_N_HOMALT AMR_FEMALE_FREQ_HOMREF  AMR_FEMALE_FREQ_HET AMR_FEMALE_FREQ_HOMALT  EAS_AN  EAS_AC  EAS_AF  EAS_N_BI_GENOS  EAS_N_HOMREF    EAS_N_HET   EAS_N_HOMALT    EAS_FREQ_HOMREF EAS_FREQ_HET    EAS_FREQ_HOMALT EAS_MALE_AN EAS_MALE_AC EAS_MALE_AF EAS_MALE_N_BI_GENOS EAS_MALE_N_HOMREF   EAS_MALE_N_HET  EAS_MALE_N_HOMALT   EAS_MALE_FREQ_HOMREF    EAS_MALE_FREQ_HET   EAS_MALE_FREQ_HOMALT    EAS_MALE_N_HEMIREF  EAS_MALE_N_HEMIALT  EAS_MALE_FREQ_HEMIREF   EAS_MALE_FREQ_HEMIALT   EAS_FEMALE_AN   EAS_FEMALE_AC   EAS_FEMALE_AF   EAS_FEMALE_N_BI_GENOS   EAS_FEMALE_N_HOMREF EAS_FEMALE_N_HET    EAS_FEMALE_N_HOMALT EAS_FEMALE_FREQ_HOMREF  EAS_FEMALE_FREQ_HET EAS_FEMALE_FREQ_HOMALT  EUR_AN  EUR_AC  EUR_AF  EUR_N_BI_GENOS  EUR_N_HOMREF    EUR_N_HET   EUR_N_HOMALT    EUR_FREQ_HOMREF EUR_FREQ_HET    EUR_FREQ_HOMALT EUR_MALE_AN EUR_MALE_AC EUR_MALE_AF EUR_MALE_N_BI_GENOS EUR_MALE_N_HOMREF   EUR_MALE_N_HET  EUR_MALE_N_HOMALT   EUR_MALE_FREQ_HOMREF    EUR_MALE_FREQ_HET   EUR_MALE_FREQ_HOMALT    EUR_MALE_N_HEMIREF  EUR_MALE_N_HEMIALT  EUR_MALE_FREQ_HEMIREF   EUR_MALE_FREQ_HEMIALT   EUR_FEMALE_AN   EUR_FEMALE_AC   EUR_FEMALE_AF   EUR_FEMALE_N_BI_GENOS   EUR_FEMALE_N_HOMREF EUR_FEMALE_N_HET    EUR_FEMALE_N_HOMALT EUR_FEMALE_FREQ_HOMREF  EUR_FEMALE_FREQ_HET EUR_FEMALE_FREQ_HOMALT  OTH_AN  OTH_AC  OTH_AF  OTH_N_BI_GENOS  OTH_N_HOMREF    OTH_N_HET   OTH_N_HOMALT    OTH_FREQ_HOMREF OTH_FREQ_HET    OTH_FREQ_HOMALT OTH_MALE_AN OTH_MALE_AC OTH_MALE_AF OTH_MALE_N_BI_GENOS OTH_MALE_N_HOMREF   OTH_MALE_N_HET  OTH_MALE_N_HOMALT   OTH_MALE_FREQ_HOMREF    OTH_MALE_FREQ_HET   OTH_MALE_FREQ_HOMALT    OTH_MALE_N_HEMIREF  OTH_MALE_N_HEMIALT  OTH_MALE_FREQ_HEMIREF   OTH_MALE_FREQ_HEMIALT   OTH_FEMALE_AN   OTH_FEMALE_AC   OTH_FEMALE_AF   OTH_FEMALE_N_BI_GENOS   OTH_FEMALE_N_HOMREF OTH_FEMALE_N_HET    OTH_FEMALE_N_HOMALT OTH_FEMALE_FREQ_HOMREF  OTH_FEMALE_FREQ_HET OTH_FEMALE_FREQ_HOMALT  FILTER
1   10641   10642   gnomAD-SV_v2.1_BND_1_1  BND manta   False   15  NA  NA  10643   10643   PE,SR   False   False   True    10642   NA  NA  NA  False   NA  NA  NA  NA  NA  NA  NA  NA  NA  -1  BND SINGLE_ENDER_-- False   False   21366   145 0.006785999983549118    10683   10543   135 5   0.9868950247764587  0.012636899948120117    0.00046803298755548894  10866   69  0.00634999992325902 5433    5366    65  2   0.987667977809906   0.011963900178670883    0.000368120992789045    NA  NA  NA  NA  False   10454   76  0.007269999943673615227 5154    70  3   0.9860339760780334  0.013392000459134579    0.0005739430198445916   0.015956999734044075    93972   0.007660999894142151    4699    4629    68  2   0.9851030111312866  0.014471200294792652    0.0004256220126990229   5154    33  0.006403000093996525    2577    2544    33  0   0.9871940016746521  0.012805599719285965    0.0NA   NA  NA  NA  4232    39  0.009216000325977802    2116    2079    35  2   0.9825140237808228  0.01654059998691082 0.0009451800142414868   1910    7   0.003664999967440963    955 949 5   1   0.9937170147895813  0.00523559981957078 0.001047119963914156    950 4   0.004211000166833401    475 472 2   1   0.9936839938163757  0.00421052984893322 0.0021052600350230932   NA  NA  NA  NA  952 3   0.0031510000117123127   476473  3   0   0.9936969876289368  0.006302520167082548    0.0 2296    31  0.013501999899744987    1148    11131   0   0.9729970097541809  0.02700350061058998 0.0 1312    13  0.009909000247716904    656 643 13  0.9801830053329468  0.01981710083782673 0.0 NA  NA  NA  NA  976 18  0.018442999571561813    488470  18  0   0.9631149768829346  0.03688519820570946 0.0 7574    32  0.004224999807775021    3787    37528   2   0.9920780062675476  0.007393720094114542    0.0005281229969114065   3374    17  0.005038999952375889    1681671 15  1   0.9905160069465637  0.008891520090401173    0.000592768017668277    NA  NA  NA  NA  41815   0.003587000072002411    2091    2077    13  1   0.9933050274848938  0.006217120215296745    0.00047823999193497188  3   0.015956999734044075    94  91  3   0   0.968084990978241   0.03191490098834038 0.0 76  0.026316000148653984    38  36  2   0   0.9473680257797241  0.05263160169124603 0.0 NA  NA  NA  NA  112 1   0.008929000236093998    56  55  1   0   0.982142984867096   0.017857100814580917    0.0UNRESOLVED      

Structural Variant Type Mapping

The source files represented the structural variants with keys using various naming conventions. In the Illumina Connected Annotations JSON output, these keys will be mapped according to the following.

Illumina Connected Annotations JSON SV Type Key	GRCh37 Source SV Type Key
copy_number_variation
deletion	DEL, CN=0
duplication	DUP
insertion	INS
inversion	INV
mobile_element_insertion	INS:ME
mobile_element_insertion	INS:ME:ALU
mobile_element_insertion	INS:ME:LINE1
mobile_element_insertion	INS:ME:SVA
structural alteration
complex_structural_alteration	CPX