Resource
| Id | Histone_ChIP-seq/ENCSR000DWV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWV [biosample_summary="Homo sapiens keratinocyte female" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN463KND|/analyses/ENCAN463KND/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF814APR|/files/ENCFF814APR/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9496750 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_not_compliant: Processed alignments file {ENCFF104YCW|/files/ENCFF104YCW/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9262072 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 {ENCFF814APR|/files/ENCFF814APR/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF814APR|/files/ENCFF814APR/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.38. 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 {ENCFF104YCW|/files/ENCFF104YCW/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF104YCW|/files/ENCFF104YCW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.50. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWV | float |
Histone_ChIP-seq_ENCSR000DWV |
Histone_ChIP-seq ENCSR000DWV [biosample_summary="Homo sapiens keratinocyte female" and target="H3K4me3"]
|
 |
[1.93, 181] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30984227 | 0.96% | 22432 |
| chr1 | 3139694 | 1.26% | 2179 |
| chr2 | 2078927 | 0.86% | 1506 |
| chr3 | 1758732 | 0.89% | 1232 |
| chr4 | 1236526 | 0.65% | 838 |
| chr5 | 1440083 | 0.79% | 993 |
| chr6 | 1826594 | 1.07% | 1326 |
| chr7 | 1442987 | 0.91% | 1065 |
| chr8 | 1120836 | 0.77% | 791 |
| chr9 | 1255776 | 0.91% | 945 |
| chr10 | 1305568 | 0.98% | 965 |
| chr11 | 1674942 | 1.24% | 1177 |
| chr12 | 1655067 | 1.24% | 1126 |
| chr13 | 587236 | 0.51% | 423 |
| chr14 | 1021458 | 0.95% | 729 |
| chr15 | 962098 | 0.94% | 696 |
| chr16 | 1227539 | 1.36% | 885 |
| chr17 | 1817623 | 2.18% | 1360 |
| chr18 | 551454 | 0.69% | 384 |
| chr19 | 2091918 | 3.57% | 1646 |
| chr20 | 814903 | 1.26% | 587 |
| chr21 | 326900 | 0.70% | 260 |
| chr22 | 705728 | 1.39% | 553 |
| chrX | 940659 | 0.60% | 764 |
| chrY | 979 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22432 | 200 | 14235 | 1381.25 | 1151 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF582JWP.bed.gz | 621.91 KB | 904f7a31945e134aa4fe686594376be1 |
| ENCFF582JWP.tabix.bed.gz | 263.09 KB | 69d74d8414be7f6daa2d93848eb34981 |
| ENCFF582JWP.tabix.bed.gz.tbi | 137.35 KB | 91f41d49872193c44a9718cdd4517816 |
| genomic_resource.yaml | 5.17 KB | 81c14beaba64c6526e0d404e7ff765e0 |
| statistics/ |