Resource
| Id | Histone_ChIP-seq/ENCSR884QDT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR884QDT [biosample_summary="Homo sapiens Loucy" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN471YBJ|/analyses/ENCAN471YBJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN471YBJ|/analyses/ENCAN471YBJ/} has in progress subobject document {2e11f00f-586e-4fb5-aa97-42dc4a5ec3b9|/documents/2e11f00f-586e-4fb5-aa97-42dc4a5ec3b9/} audit_not_compliant: Processed unfiltered alignments file {ENCFF758OGE|/files/ENCFF758OGE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 34602128 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed unfiltered alignments file {ENCFF859LLJ|/files/ENCFF859LLJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 35999647 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF643SQV|/files/ENCFF643SQV/} processed by ChIP-seq ENCODE4 v1.6.1 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 alignments file {ENCFF643SQV|/files/ENCFF643SQV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.95. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR884QDT | float |
Histone_ChIP-seq_ENCSR884QDT |
Histone_ChIP-seq ENCSR884QDT [biosample_summary="Homo sapiens Loucy" and target="H3K9me3"]
|
 |
[1.79, 12.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 21001364 | 0.65% | 37967 |
| chr1 | 1521510 | 0.61% | 2708 |
| chr2 | 1611947 | 0.67% | 2776 |
| chr3 | 1309730 | 0.66% | 2316 |
| chr4 | 1364272 | 0.72% | 2547 |
| chr5 | 848529 | 0.47% | 1601 |
| chr6 | 1319748 | 0.77% | 2379 |
| chr7 | 1469065 | 0.92% | 2768 |
| chr8 | 1193045 | 0.82% | 2242 |
| chr9 | 818904 | 0.59% | 1438 |
| chr10 | 1149680 | 0.86% | 2065 |
| chr11 | 1007422 | 0.75% | 1894 |
| chr12 | 1065988 | 0.80% | 1873 |
| chr13 | 623343 | 0.55% | 1176 |
| chr14 | 688302 | 0.64% | 1188 |
| chr15 | 657119 | 0.64% | 1170 |
| chr16 | 468661 | 0.52% | 907 |
| chr17 | 518275 | 0.62% | 969 |
| chr18 | 632570 | 0.79% | 1189 |
| chr19 | 1486885 | 2.54% | 2338 |
| chr20 | 394368 | 0.61% | 737 |
| chr21 | 394540 | 0.84% | 761 |
| chr22 | 390784 | 0.77% | 780 |
| chrX | 64612 | 0.04% | 138 |
| chrY | 2065 | <0.01% | 7 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37967 | 175 | 9497 | 553.15 | 447 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF815UIV.bed.gz | 744.24 KB | 97731a5eac621f7880b976f7877c7b2c |
| ENCFF815UIV.tabix.bed.gz | 374.71 KB | b5faf1ad34b4dad2ae085b8a55209b43 |
| ENCFF815UIV.tabix.bed.gz.tbi | 182.92 KB | dd4bf1d97e032604180ef028f6dc45a3 |
| genomic_resource.yaml | 3.92 KB | ae09ade97d3191628b4e9cb1520ba131 |
| statistics/ |