Resource
| Id | Histone_ChIP-seq/ENCSR914AWT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR914AWT [biosample_summary="Homo sapiens GM23248" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN473MIF|/analyses/ENCAN473MIF/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN473MIF|/analyses/ENCAN473MIF/} has in progress subobject document {cc0c3195-8231-462e-aca9-61724b057477|/documents/cc0c3195-8231-462e-aca9-61724b057477/} audit_warning: Processed alignments file {ENCFF988CRX|/files/ENCFF988CRX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 37712869 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: Processed alignments file {ENCFF765QXR|/files/ENCFF765QXR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 36587141 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 {ENCFF988CRX|/files/ENCFF988CRX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF988CRX|/files/ENCFF988CRX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.18. 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 {ENCFF765QXR|/files/ENCFF765QXR/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF765QXR|/files/ENCFF765QXR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.17. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR914AWT | float |
Histone_ChIP-seq_ENCSR914AWT |
Histone_ChIP-seq ENCSR914AWT [biosample_summary="Homo sapiens GM23248" and target="H3K36me3"]
|
 |
[1.6, 9.52] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 83473796 | 2.59% | 82796 |
| chr1 | 8689926 | 3.49% | 8477 |
| chr2 | 7638635 | 3.15% | 7344 |
| chr3 | 5717600 | 2.88% | 5781 |
| chr4 | 4012170 | 2.11% | 4017 |
| chr5 | 5282065 | 2.91% | 4910 |
| chr6 | 4323479 | 2.53% | 4296 |
| chr7 | 3753763 | 2.36% | 3881 |
| chr8 | 3330272 | 2.29% | 3402 |
| chr9 | 3523284 | 2.55% | 3466 |
| chr10 | 3878806 | 2.90% | 3829 |
| chr11 | 3921021 | 2.90% | 3836 |
| chr12 | 5008626 | 3.76% | 4879 |
| chr13 | 2014407 | 1.76% | 2152 |
| chr14 | 3184293 | 2.97% | 3136 |
| chr15 | 3507005 | 3.44% | 3577 |
| chr16 | 2642243 | 2.92% | 2652 |
| chr17 | 3719487 | 4.47% | 3832 |
| chr18 | 1500208 | 1.87% | 1513 |
| chr19 | 3388080 | 5.78% | 3063 |
| chr20 | 1756065 | 2.72% | 1842 |
| chr21 | 874079 | 1.87% | 889 |
| chr22 | 1258395 | 2.48% | 1357 |
| chrX | 505469 | 0.32% | 609 |
| chrY | 44418 | 0.08% | 56 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 82796 | 188 | 33716 | 1008.19 | 725 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF922AFS.bed.gz | 1.88 MB | 162024dcdde3f57b9bdaabf4b59dbd26 |
| ENCFF922AFS.tabix.bed.gz | 875.89 KB | 2daf124e51ae486400c4d5418d41868d |
| ENCFF922AFS.tabix.bed.gz.tbi | 147.61 KB | ee3645c07c347bdb1a7eabff114481c7 |
| genomic_resource.yaml | 5.23 KB | 0ce7428b5e16d6cf85bdc2bb0caa64f4 |
| statistics/ |