Resource
| Id | Histone_ChIP-seq/ENCSR000DXL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DXL [biosample_summary="Homo sapiens SK-N-MC" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN148TXW|/analyses/ENCAN148TXW/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF460OFO|/files/ENCFF460OFO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10848854 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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: Processed alignments file {ENCFF693SZI|/files/ENCFF693SZI/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11242897 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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 {ENCFF693SZI|/files/ENCFF693SZI/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF693SZI|/files/ENCFF693SZI/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.74. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DXL | float |
Histone_ChIP-seq_ENCSR000DXL |
Histone_ChIP-seq ENCSR000DXL [biosample_summary="Homo sapiens SK-N-MC" and target="H3K4me3"]
|
 |
[2.01, 149] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32130681 | 1.00% | 23275 |
| chr1 | 3158672 | 1.27% | 2211 |
| chr2 | 2235335 | 0.92% | 1581 |
| chr3 | 1760267 | 0.89% | 1204 |
| chr4 | 1335100 | 0.70% | 898 |
| chr5 | 1516758 | 0.84% | 1019 |
| chr6 | 2060641 | 1.21% | 1369 |
| chr7 | 1539685 | 0.97% | 1181 |
| chr8 | 1417589 | 0.98% | 1003 |
| chr9 | 1269202 | 0.92% | 1002 |
| chr10 | 1163114 | 0.87% | 911 |
| chr11 | 1700552 | 1.26% | 1174 |
| chr12 | 1735809 | 1.30% | 1183 |
| chr13 | 689717 | 0.60% | 473 |
| chr14 | 1106078 | 1.03% | 761 |
| chr15 | 986714 | 0.97% | 729 |
| chr16 | 1161964 | 1.29% | 933 |
| chr17 | 1802088 | 2.16% | 1358 |
| chr18 | 538904 | 0.67% | 405 |
| chr19 | 2078480 | 3.55% | 1674 |
| chr20 | 840078 | 1.30% | 629 |
| chr21 | 312214 | 0.67% | 229 |
| chr22 | 700173 | 1.38% | 574 |
| chrX | 1020957 | 0.65% | 773 |
| chrY | 590 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 23275 | 195 | 15806 | 1380.48 | 1129 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF982ERU.bed.gz | 601.81 KB | 1d7a4fcc0ea6435544cd28ac7b8c498c |
| ENCFF982ERU.tabix.bed.gz | 264.89 KB | 0ab54ba9ea6da1876041ba5b5cf1583c |
| ENCFF982ERU.tabix.bed.gz.tbi | 139.61 KB | 4d9e147923415c9ec14dec82a99369a5 |
| genomic_resource.yaml | 3.95 KB | 9d172cf6d233e412a742fbe7dbf472f6 |
| statistics/ |