Resource
| Id | Histone_ChIP-seq/ENCSR498LHL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR498LHL [biosample_summary="Homo sapiens mucosa of descending colon tissue male adult (40 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (40 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN641FJT|/analyses/ENCAN641FJT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF025OTC|/files/ENCFF025OTC/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 38189187 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF025OTC|/files/ENCFF025OTC/} processed by ChIP-seq ENCODE4 v1.8.0 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 {ENCFF025OTC|/files/ENCFF025OTC/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.85. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR498LHL | float |
Histone_ChIP-seq_ENCSR498LHL |
Histone_ChIP-seq ENCSR498LHL [biosample_summary="Homo sapiens mucosa of descending colon tissue male adult (40 years)" and target="H3K4me1"]
|
 |
[1.82, 12.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 61247440 | 1.90% | 80710 |
| chr1 | 6468930 | 2.60% | 8344 |
| chr2 | 4644161 | 1.92% | 6275 |
| chr3 | 3663103 | 1.85% | 4977 |
| chr4 | 2398169 | 1.26% | 3378 |
| chr5 | 2979126 | 1.64% | 3980 |
| chr6 | 3292901 | 1.93% | 4538 |
| chr7 | 2754249 | 1.73% | 3735 |
| chr8 | 2324456 | 1.60% | 3133 |
| chr9 | 2843533 | 2.05% | 3677 |
| chr10 | 2963542 | 2.21% | 3909 |
| chr11 | 3427768 | 2.54% | 4341 |
| chr12 | 2972635 | 2.23% | 3886 |
| chr13 | 1189047 | 1.04% | 1685 |
| chr14 | 2276599 | 2.13% | 2838 |
| chr15 | 2342636 | 2.30% | 2984 |
| chr16 | 2567755 | 2.84% | 3239 |
| chr17 | 3831428 | 4.60% | 4769 |
| chr18 | 1057848 | 1.32% | 1483 |
| chr19 | 2824116 | 4.82% | 3590 |
| chr20 | 1882990 | 2.92% | 2413 |
| chr21 | 697560 | 1.49% | 955 |
| chr22 | 1608471 | 3.17% | 2024 |
| chrX | 227977 | 0.15% | 537 |
| chrY | 8440 | 0.01% | 20 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 80710 | 175 | 16982 | 758.86 | 607 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF951XHW.bed.gz | 1.48 MB | 15d26fc3371868ab33e7c947c1d55a06 |
| ENCFF951XHW.tabix.bed.gz | 786.31 KB | 13f08bceb99cd102b396386d9ea08c6b |
| ENCFF951XHW.tabix.bed.gz.tbi | 256.23 KB | a7a78a6ef2e870455f53a7d0ea242573 |
| genomic_resource.yaml | 3.3 KB | 6ccd659ed20444c8177311754f52397a |
| statistics/ |