Resource
| Id | Histone_ChIP-seq/ENCSR000DXF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DXF [biosample_summary="Homo sapiens epithelial cell of proximal tubule" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN538MPJ|/analyses/ENCAN538MPJ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF771LTX|/files/ENCFF771LTX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17227219 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 {ENCFF247ZBG|/files/ENCFF247ZBG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16548004 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 {ENCFF771LTX|/files/ENCFF771LTX/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF771LTX|/files/ENCFF771LTX/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.05. 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 {ENCFF247ZBG|/files/ENCFF247ZBG/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF247ZBG|/files/ENCFF247ZBG/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.39. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DXF | float |
Histone_ChIP-seq_ENCSR000DXF |
Histone_ChIP-seq ENCSR000DXF [biosample_summary="Homo sapiens epithelial cell of proximal tubule" and target="H3K4me3"]
|
 |
[1.29, 149] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 45064815 | 1.40% | 34548 |
| chr1 | 4364606 | 1.75% | 3234 |
| chr2 | 3195591 | 1.32% | 2468 |
| chr3 | 2589329 | 1.31% | 1901 |
| chr4 | 1965112 | 1.03% | 1501 |
| chr5 | 2160720 | 1.19% | 1612 |
| chr6 | 2750654 | 1.61% | 2112 |
| chr7 | 2236368 | 1.40% | 1736 |
| chr8 | 1736560 | 1.20% | 1353 |
| chr9 | 1899239 | 1.37% | 1502 |
| chr10 | 1973704 | 1.48% | 1538 |
| chr11 | 2378649 | 1.76% | 1739 |
| chr12 | 2353332 | 1.77% | 1737 |
| chr13 | 972446 | 0.85% | 791 |
| chr14 | 1458640 | 1.36% | 1082 |
| chr15 | 1433755 | 1.41% | 1116 |
| chr16 | 1702049 | 1.88% | 1352 |
| chr17 | 2488916 | 2.99% | 1887 |
| chr18 | 820986 | 1.02% | 709 |
| chr19 | 2549462 | 4.35% | 2039 |
| chr20 | 1122380 | 1.74% | 842 |
| chr21 | 499028 | 1.07% | 401 |
| chr22 | 932197 | 1.83% | 737 |
| chrX | 1410503 | 0.90% | 1112 |
| chrY | 70589 | 0.12% | 47 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34548 | 170 | 31548 | 1304.41 | 866 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF671PZC.bed.gz | 932.78 KB | f0a98492d0f65d367c1d6d4c314b02e6 |
| ENCFF671PZC.tabix.bed.gz | 395.85 KB | 41504e747b495923570a0e47dd59ce4e |
| ENCFF671PZC.tabix.bed.gz.tbi | 186.64 KB | c957b536d454b0e259ef20c974f46832 |
| genomic_resource.yaml | 5.03 KB | 4da6ce1e605cdffe4070f2e6bc01c17c |
| statistics/ |