Resource
| Id | Histone_ChIP-seq/ENCSR438NCW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR438NCW [biosample_summary="Homo sapiens endocrine pancreas tissue male adult (46 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (46 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN029EYB|/analyses/ENCAN029EYB/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF632WWV|/files/ENCFF632WWV/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 5149350 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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 redacted alignments file {ENCFF632WWV|/files/ENCFF632WWV/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 redacted alignments file {ENCFF632WWV|/files/ENCFF632WWV/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR438NCW | float |
Histone_ChIP-seq_ENCSR438NCW |
Histone_ChIP-seq ENCSR438NCW [biosample_summary="Homo sapiens endocrine pancreas tissue male adult (46 years)" and target="H3K4me3"]
|
 |
[2.18, 86.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 38595790 | 1.20% | 40651 |
| chr1 | 3614525 | 1.45% | 3700 |
| chr2 | 2965257 | 1.22% | 3126 |
| chr3 | 2714350 | 1.37% | 2818 |
| chr4 | 2317444 | 1.22% | 2350 |
| chr5 | 2325561 | 1.28% | 2386 |
| chr6 | 2729612 | 1.60% | 2772 |
| chr7 | 2148163 | 1.35% | 2254 |
| chr8 | 1735424 | 1.20% | 1811 |
| chr9 | 1503448 | 1.09% | 1635 |
| chr10 | 1735180 | 1.30% | 1866 |
| chr11 | 1794925 | 1.33% | 1891 |
| chr12 | 2059904 | 1.55% | 2106 |
| chr13 | 1276038 | 1.12% | 1319 |
| chr14 | 1250403 | 1.17% | 1245 |
| chr15 | 1283404 | 1.26% | 1335 |
| chr16 | 904392 | 1.00% | 1085 |
| chr17 | 1403393 | 1.69% | 1563 |
| chr18 | 860793 | 1.07% | 920 |
| chr19 | 1132064 | 1.93% | 1369 |
| chr20 | 849940 | 1.32% | 906 |
| chr21 | 373592 | 0.80% | 412 |
| chr22 | 490612 | 0.97% | 557 |
| chrX | 1075198 | 0.69% | 1183 |
| chrY | 52168 | 0.09% | 42 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40651 | 270 | 12774 | 949.44 | 752 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF895VWP.bed.gz | 951.0 KB | 038ad0661ef10c43e7f54323e3f3b5a9 |
| ENCFF895VWP.tabix.bed.gz | 438.09 KB | fb0c93017598275ca086334125080476 |
| ENCFF895VWP.tabix.bed.gz.tbi | 207.18 KB | a3b906ee7f3838943975f8e408c8baf6 |
| genomic_resource.yaml | 3.3 KB | 83ccd1e2924975b852f38a0a5ad9e50c |
| statistics/ |