Resource
| Id | Histone_ChIP-seq/ENCSR001UVQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR001UVQ [biosample_summary="Homo sapiens mucosa of descending colon tissue male adult (40 years)" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (40 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN433EEJ|/analyses/ENCAN433EEJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF678VJD|/files/ENCFF678VJD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 41193938 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF678VJD|/files/ENCFF678VJD/} 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 {ENCFF678VJD|/files/ENCFF678VJD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR001UVQ | float |
Histone_ChIP-seq_ENCSR001UVQ |
Histone_ChIP-seq ENCSR001UVQ [biosample_summary="Homo sapiens mucosa of descending colon tissue male adult (40 years)" and target="H3K36me3"]
|
 |
[1.58, 7.54] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7822622 | 0.24% | 12223 |
| chr1 | 851159 | 0.34% | 1317 |
| chr2 | 457488 | 0.19% | 753 |
| chr3 | 400063 | 0.20% | 612 |
| chr4 | 210746 | 0.11% | 363 |
| chr5 | 321281 | 0.18% | 513 |
| chr6 | 293184 | 0.17% | 471 |
| chr7 | 324209 | 0.20% | 520 |
| chr8 | 184140 | 0.13% | 308 |
| chr9 | 337729 | 0.24% | 512 |
| chr10 | 279315 | 0.21% | 470 |
| chr11 | 452741 | 0.34% | 685 |
| chr12 | 474057 | 0.36% | 730 |
| chr13 | 101632 | 0.09% | 166 |
| chr14 | 291844 | 0.27% | 451 |
| chr15 | 277761 | 0.27% | 447 |
| chr16 | 448620 | 0.50% | 725 |
| chr17 | 565337 | 0.68% | 908 |
| chr18 | 96746 | 0.12% | 163 |
| chr19 | 852666 | 1.45% | 1152 |
| chr20 | 249856 | 0.39% | 389 |
| chr21 | 69616 | 0.15% | 120 |
| chr22 | 269443 | 0.53% | 421 |
| chrX | 12989 | 0.01% | 27 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 12223 | 230 | 7195 | 639.99 | 538 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF186VPP.bed.gz | 222.3 KB | eb89db615614bcfb34ac14e0f8d6a53b |
| ENCFF186VPP.tabix.bed.gz | 120.5 KB | 1e2b24f57ad005bed63df8a32440026f |
| ENCFF186VPP.tabix.bed.gz.tbi | 65.89 KB | f925ccbe06792b0c9e1488e298386c29 |
| genomic_resource.yaml | 3.3 KB | 84fe46ff452d9fb8962691b19ee3bac9 |
| statistics/ |