Resource
| Id | Histone_ChIP-seq/ENCSR000AQR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AQR [biosample_summary="Homo sapiens astrocyte" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 3 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN510RDO|/analyses/ENCAN510RDO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF945TQL|/files/ENCFF945TQL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15780202 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 {ENCFF755ZOD|/files/ENCFF755ZOD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 38280945 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 {ENCFF788VSD|/files/ENCFF788VSD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF788VSD|/files/ENCFF788VSD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.85. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AQR | float |
Histone_ChIP-seq_ENCSR000AQR |
Histone_ChIP-seq ENCSR000AQR [biosample_summary="Homo sapiens astrocyte" and target="H3K9me3"]
|
 |
[1.88, 14.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 15600308 | 0.48% | 40344 |
| chr1 | 894930 | 0.36% | 2368 |
| chr2 | 1136181 | 0.47% | 3144 |
| chr3 | 646670 | 0.33% | 1748 |
| chr4 | 820525 | 0.43% | 2146 |
| chr5 | 939794 | 0.52% | 2467 |
| chr6 | 663913 | 0.39% | 1871 |
| chr7 | 952544 | 0.60% | 2531 |
| chr8 | 881587 | 0.61% | 2421 |
| chr9 | 497979 | 0.36% | 1328 |
| chr10 | 932015 | 0.70% | 2503 |
| chr11 | 535328 | 0.40% | 1472 |
| chr12 | 728135 | 0.55% | 1869 |
| chr13 | 422860 | 0.37% | 1190 |
| chr14 | 420110 | 0.39% | 1161 |
| chr15 | 441716 | 0.43% | 1094 |
| chr16 | 688326 | 0.76% | 1756 |
| chr17 | 424449 | 0.51% | 1128 |
| chr18 | 421109 | 0.52% | 1126 |
| chr19 | 1868960 | 3.19% | 3742 |
| chr20 | 457451 | 0.71% | 1260 |
| chr21 | 361035 | 0.77% | 823 |
| chr22 | 310653 | 0.61% | 819 |
| chrX | 93019 | 0.06% | 256 |
| chrY | 61019 | 0.11% | 121 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40344 | 155 | 20360 | 386.68 | 318 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF755ZLD.bed.gz | 756.39 KB | 7176fcb0260b53071254c1bd3caf191d |
| ENCFF755ZLD.tabix.bed.gz | 385.49 KB | 05e9bb9b7dcc8f4c9c092ead56989f26 |
| ENCFF755ZLD.tabix.bed.gz.tbi | 199.94 KB | 89fe2a51a32dda72c7a0f418b04d05db |
| genomic_resource.yaml | 3.67 KB | ab5793beff93130e97743d5dbabee5ea |
| statistics/ |