Resource
| Id | Histone_ChIP-seq/ENCSR044WCY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR044WCY [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN032YMB|/analyses/ENCAN032YMB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF838MIE|/files/ENCFF838MIE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 34034376 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 {ENCFF225KJN|/files/ENCFF225KJN/} processed by ChIP-seq ENCODE3 hg19 pipeline has 35937474 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 {ENCFF168RVH|/files/ENCFF168RVH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF168RVH|/files/ENCFF168RVH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.66. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR044WCY | float |
Histone_ChIP-seq_ENCSR044WCY |
Histone_ChIP-seq ENCSR044WCY [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H3K9me3"]
|
 |
[1.46, 22.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33398009 | 1.04% | 121989 |
| chr1 | 2538323 | 1.02% | 9433 |
| chr2 | 2224213 | 0.92% | 8709 |
| chr3 | 1380957 | 0.70% | 5604 |
| chr4 | 1467460 | 0.77% | 5617 |
| chr5 | 1578821 | 0.87% | 6047 |
| chr6 | 1342544 | 0.79% | 5430 |
| chr7 | 2204685 | 1.38% | 7748 |
| chr8 | 1892951 | 1.30% | 6195 |
| chr9 | 1287453 | 0.93% | 4737 |
| chr10 | 1701981 | 1.27% | 6471 |
| chr11 | 1439883 | 1.07% | 5495 |
| chr12 | 1515478 | 1.14% | 5237 |
| chr13 | 847220 | 0.74% | 3117 |
| chr14 | 1187170 | 1.11% | 4175 |
| chr15 | 947823 | 0.93% | 3472 |
| chr16 | 1437086 | 1.59% | 5007 |
| chr17 | 1241654 | 1.49% | 4504 |
| chr18 | 697064 | 0.87% | 2727 |
| chr19 | 2971611 | 5.07% | 9598 |
| chr20 | 1047915 | 1.63% | 3956 |
| chr21 | 617993 | 1.32% | 2279 |
| chr22 | 997680 | 1.96% | 3158 |
| chrX | 534154 | 0.34% | 2211 |
| chrY | 295890 | 0.52% | 1062 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 121989 | 110 | 10186 | 273.78 | 218 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF085ZRB.bed.gz | 2.37 MB | 6e107e58d5ff67be599fab11b7ea9967 |
| ENCFF085ZRB.tabix.bed.gz | 1.16 MB | 5c6523467e7e85b9e910fabe7526f773 |
| ENCFF085ZRB.tabix.bed.gz.tbi | 440.22 KB | 762e0f67249bf551801dd91486086e3a |
| genomic_resource.yaml | 3.69 KB | 55970c63c8fd10bd8d7a8c9f82936783 |
| statistics/ |