Resource
| Id | Histone_ChIP-seq/ENCSR000DUK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DUK [biosample_summary="Homo sapiens HFF-Myc originated from foreskin fibroblast" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN994XNI|/analyses/ENCAN994XNI/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF263WUK|/files/ENCFF263WUK/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11586898 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: Processed alignments file {ENCFF380MQK|/files/ENCFF380MQK/} processed by ChIP-seq ENCODE3 hg19 pipeline has 12873884 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 {ENCFF263WUK|/files/ENCFF263WUK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF263WUK|/files/ENCFF263WUK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.20. 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 {ENCFF380MQK|/files/ENCFF380MQK/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF380MQK|/files/ENCFF380MQK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.65. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUK | float |
Histone_ChIP-seq_ENCSR000DUK |
Histone_ChIP-seq ENCSR000DUK [biosample_summary="Homo sapiens HFF-Myc originated from foreskin fibroblast" and target="H3K4me3"]
|
 |
[2.04, 173] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40402501 | 1.26% | 24090 |
| chr1 | 3994337 | 1.60% | 2379 |
| chr2 | 2728107 | 1.13% | 1600 |
| chr3 | 2309023 | 1.16% | 1284 |
| chr4 | 1563688 | 0.82% | 893 |
| chr5 | 1921803 | 1.06% | 1110 |
| chr6 | 2422366 | 1.42% | 1412 |
| chr7 | 1897353 | 1.19% | 1161 |
| chr8 | 1516230 | 1.04% | 918 |
| chr9 | 1665514 | 1.20% | 1036 |
| chr10 | 1691156 | 1.26% | 1027 |
| chr11 | 2189071 | 1.62% | 1230 |
| chr12 | 2224680 | 1.67% | 1260 |
| chr13 | 806861 | 0.71% | 479 |
| chr14 | 1297023 | 1.21% | 760 |
| chr15 | 1325845 | 1.30% | 793 |
| chr16 | 1643435 | 1.82% | 1009 |
| chr17 | 2351329 | 2.82% | 1441 |
| chr18 | 701437 | 0.87% | 440 |
| chr19 | 2487933 | 4.24% | 1624 |
| chr20 | 1058134 | 1.64% | 643 |
| chr21 | 415341 | 0.89% | 262 |
| chr22 | 893121 | 1.76% | 559 |
| chrX | 1247120 | 0.80% | 748 |
| chrY | 51594 | 0.09% | 22 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 24090 | 220 | 38022 | 1677.15 | 1280 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF801BZV.bed.gz | 660.55 KB | b180e22d4b463cf35a897592e384dd73 |
| ENCFF801BZV.tabix.bed.gz | 281.62 KB | d0c7bb617f93cff6755356931bf86666 |
| ENCFF801BZV.tabix.bed.gz.tbi | 142.72 KB | 7f14eaebab5c2cc3db661fd49622c6ee |
| genomic_resource.yaml | 5.06 KB | d86f5fb50225424a23cb36ab8ebe8d7f |
| statistics/ |