nstd198 - Hanlon et al 2021 - dbVar Study

nstd198 (Hanlon et al. 2021)

Organism:: Human
Study Type:: Collection
Submitter:: Vincent Hanlon
Description:: Genotyping inversions using a Bayesian binomial model (InvertypeR) and Strand-seq data published by the Human Genome Structural Variation Consortium (Chaisson et al. 2019,dbVar nstd152). Samples used: HG00512-4, HG00731-3, NA19238-40. See Variant Summary counts for nstd198 in dbVar Variant Summary.
Project:: PRJNA679815
Publication(s):: Hanlon et al. 2021
Last updated:: 2020-11-20

Links

Source: NCBI

Detailed Information: Download 234 Variant Regions, Download 3053 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	14	273	Submitted	NC_000001.11
NC_000002.12	Chr2	12	142	Submitted	NC_000002.12
NC_000003.12	Chr3	8	59	Submitted	NC_000003.12
NC_000004.12	Chr4	6	88	Submitted	NC_000004.12
NC_000005.10	Chr5	7	69	Submitted	NC_000005.10
NC_000006.12	Chr6	9	83	Submitted	NC_000006.12
NC_000007.14	Chr7	17	278	Submitted	NC_000007.14
NC_000008.11	Chr8	6	146	Submitted	NC_000008.11
NC_000009.12	Chr9	16	213	Submitted	NC_000009.12
NC_000010.11	Chr10	7	87	Submitted	NC_000010.11
NC_000011.10	Chr11	9	170	Submitted	NC_000011.10
NC_000012.12	Chr12	9	101	Submitted	NC_000012.12
NC_000013.11	Chr13	4	54	Submitted	NC_000013.11
NC_000014.9	Chr14	6	38	Submitted	NC_000014.9
NC_000015.10	Chr15	10	106	Submitted	NC_000015.10
NC_000016.10	Chr16	12	249	Submitted	NC_000016.10
NC_000017.11	Chr17	10	83	Submitted	NC_000017.11
NC_000018.10	Chr18	2	31	Submitted	NC_000018.10
NC_000019.10	Chr19	1	18	Submitted	NC_000019.10
NC_000020.11	Chr20	6	43	Submitted	NC_000020.11
NC_000021.9	Chr21	6	56	Submitted	NC_000021.9
NC_000022.11	Chr22	9	79	Submitted	NC_000022.11
NC_000023.11	ChrX	31	541	Submitted	NC_000023.11
NC_000024.10	ChrY	17	46	Submitted	NC_000024.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	10	233	Remapped	NC_000001.10
NC_000002.11	Chr2	12	139	Remapped	NC_000002.11
NC_000003.11	Chr3	8	59	Remapped	NC_000003.11
NC_000004.11	Chr4	6	88	Remapped	NC_000004.11
NC_000005.9	Chr5	6	63	Remapped	NC_000005.9
NC_000006.11	Chr6	8	82	Remapped	NC_000006.11
NC_000007.13	Chr7	15	264	Remapped	NC_000007.13
NC_000008.10	Chr8	5	116	Remapped	NC_000008.10
NC_000009.11	Chr9	13	186	Remapped	NC_000009.11
NC_000010.10	Chr10	6	73	Remapped	NC_000010.10
NC_000011.9	Chr11	9	170	Remapped	NC_000011.9
NC_000012.11	Chr12	8	94	Remapped	NC_000012.11
NC_000013.10	Chr13	3	26	Remapped	NC_000013.10
NC_000014.8	Chr14	6	38	Remapped	NC_000014.8
NC_000015.9	Chr15	8	73	Remapped	NC_000015.9
NC_000016.9	Chr16	12	241	Remapped	NC_000016.9
NC_000017.10	Chr17	5	60	Remapped	NC_000017.10
NC_000018.9	Chr18	1	23	Remapped	NC_000018.9
NC_000019.9	Chr19	1	18	Remapped	NC_000019.9
NC_000020.10	Chr20	3	22	Remapped	NC_000020.10
NC_000021.8	Chr21	5	44	Remapped	NC_000021.8
NC_000022.10	Chr22	8	61	Remapped	NC_000022.10
NC_000023.10	ChrX	24	476	Remapped	NC_000023.10
NC_000024.9	ChrY	16	40	Remapped	NC_000024.9
NT_113923.1	Unplaced\|NT_113923.1	0	27	Remapped	NT_113923.1
NT_167207.1	Chr1\|NT_167207.1	0	1	Remapped	NT_167207.1
NW_003871055.3	Chr1\|NW_003871055.3	4	114	Remapped	NW_003871055.3
NW_003871056.3	Chr1\|NW_003871056.3	1	36	Remapped	NW_003871056.3
NW_004070866.1	Chr6\|NW_004070866.1	1	20	Remapped	NW_004070866.1
NW_004504300.1	Chr6\|NW_004504300.1	1	29	Remapped	NW_004504300.1
NW_003871064.1	Chr7\|NW_003871064.1	1	12	Remapped	NW_003871064.1
NW_004775430.1	Chr7\|NW_004775430.1	0	6	Remapped	NW_004775430.1
NW_003571042.1	Chr8\|NW_003571042.1	0	2	Remapped	NW_003571042.1
NT_113916.2	Chr9\|NT_113916.2	0	2	Remapped	NT_113916.2
NW_003871068.1	Chr10\|NW_003871068.1	1	14	Remapped	NW_003871068.1
NW_003871071.1	Chr10\|NW_003871071.1	1	8	Remapped	NW_003871071.1
NW_004166863.1	Chr14\|NW_004166863.1	1	2	Remapped	NW_004166863.1
NW_003315949.1	Chr17\|NW_003315949.1	3	3	Remapped	NW_003315949.1
NW_003871100.1	ChrX\|NW_003871100.1	1	14	Remapped	NW_003871100.1
NW_003871103.3	ChrX\|NW_003871103.3	5	92	Remapped	NW_003871103.3
NW_004070877.1	ChrX\|NW_004070877.1	5	125	Remapped	NW_004070877.1
NW_004070880.2	ChrX\|NW_004070880.2	1	7	Remapped	NW_004070880.2
NW_004070881.1	ChrX\|NW_004070881.1	1	16	Remapped	NW_004070881.1
NW_004070882.1	ChrX\|NW_004070882.1	2	19	Remapped	NW_004070882.1
NW_004070883.1	ChrX\|NW_004070883.1	1	32	Remapped	NW_004070883.1
NW_004070884.1	ChrX\|NW_004070884.1	1	18	Remapped	NW_004070884.1
NW_004070885.1	ChrX\|NW_004070885.1	1	32	Remapped	NW_004070885.1
NW_004070886.1	ChrX\|NW_004070886.1	1	8	Remapped	NW_004070886.1
NW_004070887.1	ChrX\|NW_004070887.1	3	28	Remapped	NW_004070887.1
NW_004070888.1	ChrX\|NW_004070888.1	2	4	Remapped	NW_004070888.1
NW_004070890.2	ChrX\|NW_004070890.2	1	50	Remapped	NW_004070890.2
NW_004070892.1	ChrX\|NW_004070892.1	0	18	Remapped	NW_004070892.1

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.11	Chr1	14	11	0	1	1	1	273	135	14	15	1	108
NC_000002.12	Chr2	12	9	1	2	0	0	142	126	6	7	3	0
NC_000003.12	Chr3	8	8	0	0	0	0	59	59	0	0	0	0
NC_000004.12	Chr4	6	6	0	0	0	0	88	88	0	0	0	0
NC_000005.10	Chr5	7	6	0	0	1	0	69	63	0	0	6	0
NC_000006.12	Chr6	9	8	0	0	0	1	83	35	0	0	0	48
NC_000007.14	Chr7	17	13	1	2	1	0	278	184	11	68	9	6
NC_000008.11	Chr8	6	4	0	1	1	0	146	113	0	5	28	0
NC_000009.12	Chr9	16	8	0	4	3	1	213	119	6	57	27	4
NC_000010.11	Chr10	7	5	1	0	0	1	87	76	3	0	0	8
NC_000011.10	Chr11	9	8	0	1	0	0	170	142	0	28	0	0
NC_000012.12	Chr12	9	7	1	0	1	0	101	93	1	0	7	0
NC_000013.11	Chr13	4	3	0	0	1	0	54	51	0	2	1	0
NC_000014.9	Chr14	6	5	0	0	0	1	38	36	0	0	0	2
NC_000015.10	Chr15	10	5	1	2	2	0	106	31	9	33	33	0
NC_000016.10	Chr16	12	9	2	1	0	0	249	201	4	30	6	8
NC_000017.11	Chr17	10	5	2	1	2	0	83	60	2	1	20	0
NC_000018.10	Chr18	2	1	0	0	1	0	31	23	0	0	8	0
NC_000019.10	Chr19	1	1	0	0	0	0	18	18	0	0	0	0
NC_000020.11	Chr20	6	3	0	0	3	0	43	22	0	2	19	0
NC_000021.9	Chr21	6	4	0	0	2	0	56	32	4	2	18	0
NC_000022.11	Chr22	9	6	0	2	0	1	79	41	3	20	9	6
NC_000023.11	ChrX	31	9	0	0	2	20	541	113	6	12	6	404
NC_000024.10	ChrY	17	15	1	0	1	0	46	38	2	0	6	0

Samplesets

Number of Samplesets: 1

Size:: 9
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
SAMN00006466	HG00513	Female	CHS	Not reported
SAMN00001695	NA19239	Male	YRI	Not reported
SAMN00001696	NA19240	Female	YRI	Not reported
SAMN00001694	NA19238	Female	YRI	Not reported
HG00512	HG00512	Male	CHS	Not reported
SAMN00006579	HG00731	Male	PUR	Not reported
SAMN00006580	HG00732	Female	PUR	Not reported
HG00514	HG00514	Female	CHS	Not reported
SAMN00006581	HG00733	Female	PUR	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Genotyping	Sequencing	Genotyping	3,053

dbVar

Database of genomic structural variation

nstd198 (Hanlon et al. 2021)

Links

Detailed Information: Download 234 Variant Regions, Download 3053 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd198 (Hanlon et al. 2021)

Links

Detailed Information: Download 234 Variant Regions, Download 3053 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38 (hg38)GRCh37.p13 (hg19)

Remapping summary: GRCh38->GRCh37.p13

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: