Resource
| Id | Histone_ChIP-seq/ENCSR386JEL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR386JEL [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (17 weeks) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN549GOL|/analyses/ENCAN549GOL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF226JND|/files/ENCFF226JND/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 21940927 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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_not_compliant: Processed redacted alignments file {ENCFF623UKD|/files/ENCFF623UKD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 29171834 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 redacted alignments file {ENCFF226JND|/files/ENCFF226JND/} processed by ChIP-seq ENCODE3 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 redacted alignments file {ENCFF226JND|/files/ENCFF226JND/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR386JEL | float |
Histone_ChIP-seq_ENCSR386JEL |
Histone_ChIP-seq ENCSR386JEL [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K4me1"]
|
 |
[1.84, 12.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 78330259 | 2.43% | 123832 |
| chr1 | 7771797 | 3.12% | 11724 |
| chr1_KI270713v1_random | 598 | 1.47% | 2 |
| chr2 | 6318028 | 2.61% | 10259 |
| chr3 | 4579096 | 2.31% | 7718 |
| chr4 | 2821903 | 1.48% | 5029 |
| chr5 | 4036251 | 2.22% | 6690 |
| chr6 | 4181397 | 2.45% | 7017 |
| chr7 | 3897338 | 2.45% | 6473 |
| chr8 | 3535980 | 2.44% | 6043 |
| chr9 | 3606936 | 2.61% | 5495 |
| chr10 | 3831174 | 2.86% | 6137 |
| chr11 | 4841161 | 3.58% | 7179 |
| chr12 | 3850773 | 2.89% | 6140 |
| chr13 | 1701210 | 1.49% | 2996 |
| chr14 | 2785243 | 2.60% | 4301 |
| chr15 | 2690589 | 2.64% | 4179 |
| chr16 | 3069471 | 3.40% | 4595 |
| chr17 | 4152990 | 4.99% | 5719 |
| chr17_GL000205v2_random | 444 | 0.24% | 1 |
| chr18 | 1777812 | 2.21% | 3072 |
| chr19 | 2812358 | 4.80% | 3843 |
| chr20 | 2464107 | 3.82% | 3681 |
| chr21 | 722997 | 1.55% | 1204 |
| chr22 | 2285953 | 4.50% | 3097 |
| chrUn_GL000195v1 | 1213 | 0.66% | 3 |
| chrX | 593440 | 0.38% | 1235 |
| 3340 contigs with no values (185895268 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 123832 | 190 | 11461 | 632.55 | 475 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF272XDQ.bed.gz | 2.18 MB | 5baef7bb26e1f700ca23b14a38b747d9 |
| ENCFF272XDQ.tabix.bed.gz | 1.15 MB | 74e5216700aaed9ce146406e103d68d2 |
| ENCFF272XDQ.tabix.bed.gz.tbi | 366.32 KB | eb9a2b338d2dfec7f47024ccbbadc5d9 |
| genomic_resource.yaml | 3.75 KB | acafe684d4d45e830b2a120905e745b6 |
| statistics/ |