Resource
| Id | Histone_ChIP-seq/ENCSR000ALW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ALW [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (50 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN532TFF|/analyses/ENCAN532TFF/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF807VEH|/files/ENCFF807VEH/} processed by ChIP-seq ENCODE3 hg19 pipeline has 7439983 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-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 {ENCFF674SDM|/files/ENCFF674SDM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9853373 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-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 {ENCFF807VEH|/files/ENCFF807VEH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF807VEH|/files/ENCFF807VEH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 4.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ALW | float |
Histone_ChIP-seq_ENCSR000ALW |
Histone_ChIP-seq ENCSR000ALW [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="H3K27ac"]
|
 |
[1.77, 90.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 66057311 | 2.05% | 65537 |
| chr1 | 6409048 | 2.57% | 6336 |
| chr2 | 5384731 | 2.22% | 5361 |
| chr3 | 4582054 | 2.31% | 4416 |
| chr4 | 3392238 | 1.78% | 3248 |
| chr5 | 3694669 | 2.04% | 3508 |
| chr6 | 4248793 | 2.49% | 4095 |
| chr7 | 3219698 | 2.02% | 3196 |
| chr8 | 2989425 | 2.06% | 3040 |
| chr9 | 2614224 | 1.89% | 2748 |
| chr10 | 3148086 | 2.35% | 3037 |
| chr11 | 3384247 | 2.51% | 3297 |
| chr12 | 3761810 | 2.82% | 3523 |
| chr13 | 1579568 | 1.38% | 1623 |
| chr14 | 2129437 | 1.99% | 2038 |
| chr15 | 2131966 | 2.09% | 2121 |
| chr16 | 1880118 | 2.08% | 2099 |
| chr17 | 2761634 | 3.32% | 2817 |
| chr18 | 1575335 | 1.96% | 1521 |
| chr19 | 1921789 | 3.28% | 2126 |
| chr20 | 1708680 | 2.65% | 1722 |
| chr21 | 841293 | 1.80% | 812 |
| chr22 | 1121220 | 2.21% | 1108 |
| chrX | 1576660 | 1.01% | 1744 |
| chrY | 588 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 65537 | 180 | 16579 | 1007.94 | 677 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF360PVA.bed.gz | 1.62 MB | d492ced5c246be0a9b8bda3af592b867 |
| ENCFF360PVA.tabix.bed.gz | 722.07 KB | edc479ae19e72e33df06ef7fbbb6325e |
| ENCFF360PVA.tabix.bed.gz.tbi | 236.71 KB | 58eec65e7a8b6972f0fd0bab8e55f3b6 |
| genomic_resource.yaml | 3.73 KB | f39244bd5f17d06e841f03a35c6ae42e |
| statistics/ |