Resource
| Id | Histone_ChIP-seq/ENCSR000DUO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN506YWM|/analyses/ENCAN506YWM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7623406 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_not_compliant: Processed alignments file {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9161715 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 {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.95. 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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.20. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUO | float |
Histone_ChIP-seq_ENCSR000DUO |
Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"]
|
 |
[2.09, 184] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29213082 | 0.91% | 24705 |
| chr1 | 2913419 | 1.17% | 2454 |
| chr1_KI270712v1_random | 1901 | 1.08% | 3 |
| chr2 | 1966558 | 0.81% | 1651 |
| chr3 | 1648659 | 0.83% | 1325 |
| chr4 | 1113176 | 0.59% | 869 |
| chr5 | 1311669 | 0.72% | 1095 |
| chr6 | 1682906 | 0.99% | 1360 |
| chr7 | 1407626 | 0.88% | 1243 |
| chr8 | 1077003 | 0.74% | 879 |
| chr9 | 1209103 | 0.87% | 1071 |
| chr10 | 1154085 | 0.86% | 939 |
| chr11 | 1609983 | 1.19% | 1285 |
| chr12 | 1572771 | 1.18% | 1271 |
| chr13 | 628489 | 0.55% | 501 |
| chr14 | 923574 | 0.86% | 810 |
| chr15 | 973590 | 0.95% | 834 |
| chr16 | 1207919 | 1.34% | 1039 |
| chr17 | 1712945 | 2.06% | 1534 |
| chr17_GL000205v2_random | 1891 | 1.02% | 2 |
| chr18 | 490699 | 0.61% | 390 |
| chr19 | 1957609 | 3.34% | 1808 |
| chr20 | 771220 | 1.20% | 660 |
| chr21 | 296860 | 0.64% | 251 |
| chr22 | 686311 | 1.35% | 604 |
| chrUn_GL000219v1 | 1320 | 0.74% | 2 |
| chrUn_GL000220v1 | 297 | 0.18% | 1 |
| chrX | 891499 | 0.57% | 824 |
| 3339 contigs with no values (185601866 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 24705 | 155 | 11126 | 1182.48 | 903 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF034USW.bed.gz | 665.25 KB | 488ff0debfd714b9b780ad391b56e9d9 |
| ENCFF034USW.tabix.bed.gz | 284.28 KB | 16af41c3dbe669b545a33b9363e3130d |
| ENCFF034USW.tabix.bed.gz.tbi | 135.56 KB | e2ba29d8ec437ea80b51b4145a6ca65c |
| genomic_resource.yaml | 5.27 KB | 4462263a44e0b23fbc0e30ff44a2e858 |
| statistics/ |