Resource
| Id | Histone_ChIP-seq/ENCSR000DTQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DTQ [biosample_summary="Homo sapiens HCT116" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Released analysis {ENCAN614HNE|/analyses/ENCAN614HNE/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN614HNE|/analyses/ENCAN614HNE/} has in progress subobject document {59538a9c-dfd6-46d7-9c56-72be9eaea02c|/documents/59538a9c-dfd6-46d7-9c56-72be9eaea02c/} audit_warning: Processed alignments file {ENCFF013LEY|/files/ENCFF013LEY/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 18916015 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 alignments file {ENCFF013LEY|/files/ENCFF013LEY/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF013LEY|/files/ENCFF013LEY/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.37. 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 {ENCFF178XNO|/files/ENCFF178XNO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF178XNO|/files/ENCFF178XNO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.43. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DTQ | float |
Histone_ChIP-seq_ENCSR000DTQ |
Histone_ChIP-seq ENCSR000DTQ [biosample_summary="Homo sapiens HCT116" and target="H3K4me3"]
|
 |
[1.89, 121] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33014937 | 1.03% | 25621 |
| chr1 | 3314755 | 1.33% | 2558 |
| chr2 | 2180277 | 0.90% | 1733 |
| chr3 | 1788813 | 0.90% | 1328 |
| chr4 | 1249486 | 0.66% | 945 |
| chr5 | 1438932 | 0.79% | 1072 |
| chr6 | 1812192 | 1.06% | 1402 |
| chr7 | 1603403 | 1.01% | 1262 |
| chr8 | 1207477 | 0.83% | 922 |
| chr9 | 1348487 | 0.97% | 1083 |
| chr10 | 1393771 | 1.04% | 1105 |
| chr11 | 1784798 | 1.32% | 1320 |
| chr12 | 1758826 | 1.32% | 1324 |
| chr13 | 601118 | 0.53% | 474 |
| chr14 | 1049890 | 0.98% | 815 |
| chr15 | 1017399 | 1.00% | 795 |
| chr16 | 1470759 | 1.63% | 1150 |
| chr17 | 2111668 | 2.54% | 1586 |
| chr18 | 498055 | 0.62% | 402 |
| chr19 | 2381649 | 4.06% | 1883 |
| chr20 | 893502 | 1.39% | 727 |
| chr21 | 282124 | 0.60% | 239 |
| chr22 | 844443 | 1.66% | 684 |
| chrX | 953252 | 0.61% | 786 |
| chrY | 29861 | 0.05% | 26 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25621 | 158 | 9392 | 1288.59 | 1079 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF187LLD.bed.gz | 651.87 KB | a9df0277b6f3fe0f5dbb9e72a2d37f77 |
| ENCFF187LLD.tabix.bed.gz | 291.62 KB | a6afffe9101404510c29c6f9ca821154 |
| ENCFF187LLD.tabix.bed.gz.tbi | 141.08 KB | 53e5c11e5f09f334e403f1625a42d351 |
| genomic_resource.yaml | 4.72 KB | ad15be60d4752b61d7d9dd5c5431d915 |
| statistics/ |