Resource
| Id | Histone_ChIP-seq/ENCSR000DVS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DVS [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN425MYE|/analyses/ENCAN425MYE/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18935038 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 {ENCFF398APA|/files/ENCFF398APA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19621928 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 {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF336RRY|/files/ENCFF336RRY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.19. 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 {ENCFF398APA|/files/ENCFF398APA/} 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 {ENCFF398APA|/files/ENCFF398APA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.23. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DVS | float |
Histone_ChIP-seq_ENCSR000DVS |
Histone_ChIP-seq ENCSR000DVS [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="H3K4me3"]
|
 |
[1.88, 130] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41063847 | 1.28% | 36149 |
| chr1 | 3923395 | 1.58% | 3404 |
| chr1_KI270712v1_random | 524 | 0.30% | 2 |
| chr1_KI270713v1_random | 154 | 0.38% | 1 |
| chr1_KI270714v1_random | 172 | 0.41% | 1 |
| chr2 | 2823927 | 1.17% | 2482 |
| chr3 | 2318724 | 1.17% | 1953 |
| chr4 | 1729109 | 0.91% | 1526 |
| chr5 | 2025263 | 1.12% | 1720 |
| chr6 | 2451206 | 1.44% | 2052 |
| chr7 | 2003794 | 1.26% | 1747 |
| chr8 | 1587935 | 1.09% | 1437 |
| chr9 | 1677243 | 1.21% | 1508 |
| chr10 | 1713462 | 1.28% | 1594 |
| chr11 | 2195950 | 1.63% | 1834 |
| chr12 | 2219914 | 1.67% | 1867 |
| chr13 | 900535 | 0.79% | 859 |
| chr14 | 1328683 | 1.24% | 1142 |
| chr14_GL000194v1_random | 263 | 0.14% | 1 |
| chr15 | 1367857 | 1.34% | 1195 |
| chr16 | 1583909 | 1.75% | 1465 |
| chr16_KI270728v1_random | 264 | 0.01% | 1 |
| chr17 | 2338388 | 2.81% | 2132 |
| chr17_GL000205v2_random | 2092 | 1.13% | 3 |
| chr18 | 718272 | 0.89% | 696 |
| chr19 | 2535776 | 4.33% | 2263 |
| chr20 | 1035346 | 1.61% | 919 |
| chr21 | 412063 | 0.88% | 405 |
| chr22 | 865247 | 1.70% | 810 |
| chr22_KI270732v1_random | 538 | 1.30% | 1 |
| chr22_KI270733v1_random | 263 | 0.15% | 1 |
| chrUn_GL000195v1 | 313 | 0.17% | 2 |
| chrUn_GL000218v1 | 252 | 0.16% | 1 |
| chrUn_GL000219v1 | 3060 | 1.71% | 4 |
| chrUn_GL000220v1 | 259 | 0.16% | 1 |
| chrUn_KI270442v1 | 299 | 0.08% | 2 |
| chrUn_KI270744v1 | 243 | 0.14% | 1 |
| chrX | 1253730 | 0.80% | 1091 |
| chrY | 45423 | 0.08% | 26 |
| 3328 contigs with no values (125101870 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36149 | 145 | 29679 | 1135.96 | 675 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF622AJL.bed.gz | 900.58 KB | 0f1b56f5e229eba2c1b2c61fe41f0834 |
| ENCFF622AJL.tabix.bed.gz | 399.51 KB | de10abf6c050ab647e97828ac006e698 |
| ENCFF622AJL.tabix.bed.gz.tbi | 183.22 KB | 5c720b21f89286e63384540360847795 |
| genomic_resource.yaml | 5.04 KB | 1988524040214f6fe52c0347b15e1d68 |
| statistics/ |