Resource
| Id | Histone_ChIP-seq/ENCSR000ALX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ALX [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (50 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN407JAU|/analyses/ENCAN407JAU/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN407JAU|/analyses/ENCAN407JAU/} has in progress subobject document {ac0d55c0-aa50-4bb5-b075-6d0de38938f6|/documents/ac0d55c0-aa50-4bb5-b075-6d0de38938f6/} audit_not_compliant: Processed alignments file {ENCFF730XKI|/files/ENCFF730XKI/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 6667208 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 alignments file {ENCFF034GVN|/files/ENCFF034GVN/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 8026132 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 alignments file {ENCFF034GVN|/files/ENCFF034GVN/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 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 {ENCFF034GVN|/files/ENCFF034GVN/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ALX | float |
Histone_ChIP-seq_ENCSR000ALX |
Histone_ChIP-seq ENCSR000ALX [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="H3K27me3"]
|
 |
[2.19, 16.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 18332446 | 0.57% | 51063 |
| chr1 | 1613791 | 0.65% | 4398 |
| chr2 | 1472092 | 0.61% | 4047 |
| chr3 | 1065725 | 0.54% | 3109 |
| chr4 | 1223010 | 0.64% | 3538 |
| chr5 | 1084962 | 0.60% | 3119 |
| chr6 | 1251986 | 0.73% | 3542 |
| chr7 | 1055972 | 0.66% | 2958 |
| chr8 | 835813 | 0.58% | 2410 |
| chr9 | 751687 | 0.54% | 2042 |
| chr10 | 888816 | 0.66% | 2311 |
| chr11 | 996849 | 0.74% | 2682 |
| chr12 | 805779 | 0.60% | 2318 |
| chr13 | 539463 | 0.47% | 1457 |
| chr14 | 499540 | 0.47% | 1262 |
| chr15 | 518583 | 0.51% | 1276 |
| chr16 | 366493 | 0.41% | 951 |
| chr17 | 687823 | 0.83% | 1591 |
| chr18 | 424036 | 0.53% | 1267 |
| chr19 | 340550 | 0.58% | 810 |
| chr20 | 543106 | 0.84% | 1398 |
| chr21 | 163572 | 0.35% | 423 |
| chr22 | 188662 | 0.37% | 512 |
| chrX | 1014136 | 0.65% | 3642 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51063 | 143 | 7993 | 359.02 | 261 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF518UWB.bed.gz | 933.07 KB | 9cad3e8cb0579131c0facbc00d27031d |
| ENCFF518UWB.tabix.bed.gz | 479.5 KB | a281a015cd59fc43e51067ae1862decc |
| ENCFF518UWB.tabix.bed.gz.tbi | 213.83 KB | 043baa5266fd6e08f6c76f875b43716b |
| genomic_resource.yaml | 3.99 KB | 70721ff0061502fb7321056c31d9e526 |
| statistics/ |