Resource
| Id | Histone_ChIP-seq/ENCSR000DVN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DVN [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: newborn output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN684XIM|/analyses/ENCAN684XIM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF288CHB|/files/ENCFF288CHB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10738235 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 {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15521940 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 {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.07. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DVN | float |
Histone_ChIP-seq_ENCSR000DVN |
Histone_ChIP-seq ENCSR000DVN [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K4me3"]
|
 |
[2.01, 106] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 27569011 | 0.86% | 22934 |
| chr1 | 2689374 | 1.08% | 2231 |
| chr1_KI270712v1_random | 465 | 0.26% | 2 |
| chr2 | 1865381 | 0.77% | 1502 |
| chr3 | 1586032 | 0.80% | 1252 |
| chr4 | 1119002 | 0.59% | 869 |
| chr5 | 1300131 | 0.72% | 1024 |
| chr6 | 1626607 | 0.95% | 1325 |
| chr7 | 1398961 | 0.88% | 1198 |
| chr8 | 1020422 | 0.70% | 816 |
| chr9 | 1152660 | 0.83% | 952 |
| chr10 | 1156613 | 0.86% | 947 |
| chr11 | 1454611 | 1.08% | 1186 |
| chr12 | 1460433 | 1.10% | 1171 |
| chr13 | 552942 | 0.48% | 435 |
| chr14 | 900393 | 0.84% | 729 |
| chr15 | 900670 | 0.88% | 750 |
| chr16 | 1077267 | 1.19% | 922 |
| chr17 | 1576120 | 1.89% | 1365 |
| chr17_GL000205v2_random | 2035 | 1.10% | 2 |
| chr18 | 461974 | 0.57% | 354 |
| chr19 | 1732682 | 2.96% | 1713 |
| chr20 | 711200 | 1.10% | 593 |
| chr21 | 263348 | 0.56% | 225 |
| chr22 | 609920 | 1.20% | 534 |
| chrUn_GL000195v1 | 326 | 0.18% | 2 |
| chrUn_GL000219v1 | 1364 | 0.76% | 2 |
| chrUn_GL000220v1 | 308 | 0.19% | 1 |
| chrX | 916289 | 0.59% | 808 |
| chrY | 31481 | 0.06% | 24 |
| 3337 contigs with no values (128191555 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22934 | 160 | 16044 | 1202.1 | 1007.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF657MIQ.bed.gz | 632.34 KB | 9e55ae38241a1fcfa1f6e75776fcd482 |
| ENCFF657MIQ.tabix.bed.gz | 267.69 KB | 955b1d7a74a64923c5fa11016346beea |
| ENCFF657MIQ.tabix.bed.gz.tbi | 137.23 KB | 5726c9584edb8bafec403a4fea3cb969 |
| genomic_resource.yaml | 4.15 KB | 2511dcd56afc1ca639e4c6c4b5b0fb11 |
| statistics/ |