Resource
| Id | Histone_ChIP-seq/ENCSR000ALC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ALC [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: newborn output_type: replicated peaks audit_error: Processed alignments file {ENCFF571XAD|/files/ENCFF571XAD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 999999 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_internal_action: Archived analysis {ENCAN586WEO|/analyses/ENCAN586WEO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF449FVX|/files/ENCFF449FVX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 5403144 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed alignments file {ENCFF140AOS|/files/ENCFF140AOS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 7896082 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments. 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 {ENCFF571XAD|/files/ENCFF571XAD/} 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 {ENCFF571XAD|/files/ENCFF571XAD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.13. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ALC | float |
Histone_ChIP-seq_ENCSR000ALC |
Histone_ChIP-seq ENCSR000ALC [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K36me3"]
|
 |
[1.68, 13.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 37703683 | 1.17% | 69130 |
| chr1 | 3989019 | 1.60% | 7056 |
| chr2 | 3220603 | 1.33% | 5850 |
| chr3 | 2580819 | 1.30% | 4731 |
| chr4 | 1717445 | 0.90% | 3199 |
| chr5 | 2113458 | 1.16% | 3803 |
| chr6 | 1826815 | 1.07% | 3381 |
| chr7 | 1659482 | 1.04% | 3067 |
| chr8 | 1330330 | 0.92% | 2552 |
| chr9 | 1513198 | 1.09% | 2765 |
| chr10 | 1769758 | 1.32% | 3163 |
| chr11 | 1841154 | 1.36% | 3354 |
| chr12 | 2424433 | 1.82% | 4308 |
| chr13 | 973235 | 0.85% | 1801 |
| chr14 | 1436436 | 1.34% | 2629 |
| chr15 | 1442629 | 1.41% | 2658 |
| chr16 | 1403366 | 1.55% | 2597 |
| chr17 | 1900490 | 2.28% | 3483 |
| chr18 | 599742 | 0.75% | 1184 |
| chr19 | 1205654 | 2.06% | 2319 |
| chr20 | 1052806 | 1.63% | 1938 |
| chr21 | 474017 | 1.01% | 905 |
| chr22 | 854011 | 1.68% | 1535 |
| chrX | 357255 | 0.23% | 815 |
| chrY | 17528 | 0.03% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 69130 | 190 | 8839 | 545.4 | 451 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF594LVO.bed.gz | 1.31 MB | 1aa27998e808c274c366578a6a1103f1 |
| ENCFF594LVO.tabix.bed.gz | 672.0 KB | 1a906b1028e499f462299866d94f61e2 |
| ENCFF594LVO.tabix.bed.gz.tbi | 144.92 KB | d7330eb319563e8124a0d3b08540a154 |
| genomic_resource.yaml | 4.33 KB | e51dbbf92013081ec8822d4f6aaafd00 |
| statistics/ |