Resource
| Id | Histone_ChIP-seq/ENCSR001SHB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR001SHB [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN214RHK|/analyses/ENCAN214RHK/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF735KUK|/files/ENCFF735KUK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15333347 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF735KUK|/files/ENCFF735KUK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF735KUK|/files/ENCFF735KUK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.69. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR001SHB | float |
Histone_ChIP-seq_ENCSR001SHB |
Histone_ChIP-seq ENCSR001SHB [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K27ac"]
|
 |
[1.77, 41.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 31068755 | 0.97% | 38407 |
| chr1 | 3433521 | 1.38% | 4065 |
| chr1_KI270713v1_random | 334 | 0.82% | 1 |
| chr2 | 2042336 | 0.84% | 2646 |
| chr3 | 1716146 | 0.87% | 2217 |
| chr4 | 1063246 | 0.56% | 1366 |
| chr5 | 1415263 | 0.78% | 1808 |
| chr6 | 1589387 | 0.93% | 2022 |
| chr7 | 1312343 | 0.82% | 1675 |
| chr8 | 1142203 | 0.79% | 1507 |
| chr9 | 1406856 | 1.02% | 1719 |
| chr10 | 1367215 | 1.02% | 1703 |
| chr11 | 1828310 | 1.35% | 2174 |
| chr12 | 1499158 | 1.12% | 1827 |
| chr13 | 593076 | 0.52% | 773 |
| chr14 | 1076471 | 1.01% | 1317 |
| chr15 | 1089031 | 1.07% | 1330 |
| chr16 | 1288210 | 1.43% | 1640 |
| chr17 | 2074500 | 2.49% | 2383 |
| chr18 | 536396 | 0.67% | 684 |
| chr19 | 1747574 | 2.98% | 2088 |
| chr20 | 880084 | 1.37% | 1092 |
| chr21 | 382857 | 0.82% | 500 |
| chr22 | 918428 | 1.81% | 1006 |
| chrM | 4426 | 26.71% | 7 |
| chrUn_GL000219v1 | 1449 | 0.81% | 2 |
| chrX | 633363 | 0.41% | 826 |
| chrY | 26572 | 0.05% | 29 |
| 3339 contigs with no values (128840573 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38407 | 180 | 11217 | 808.93 | 587 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF598JDA.bed.gz | 916.99 KB | ae1e164a720202f442f3713596a73c3e |
| ENCFF598JDA.tabix.bed.gz | 414.49 KB | dec4a4b869970b7829385c7072c65802 |
| ENCFF598JDA.tabix.bed.gz.tbi | 160.7 KB | 1f0e5d7cda80e0f7beafbcee28b1b753 |
| genomic_resource.yaml | 3.22 KB | 4e5d010abb53ca203d242755260a981c |
| statistics/ |