Resource
| Id | Histone_ChIP-seq/ENCSR000ARX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ARX [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN389UPU|/analyses/ENCAN389UPU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF584VOZ|/files/ENCFF584VOZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 5624559 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed unfiltered alignments file {ENCFF766WYG|/files/ENCFF766WYG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 42964639 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF506WJB|/files/ENCFF506WJB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF506WJB|/files/ENCFF506WJB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.98. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ARX | float |
Histone_ChIP-seq_ENCSR000ARX |
Histone_ChIP-seq ENCSR000ARX [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K9me3"]
|
 |
[1.66, 8.84] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 1341144 | 0.04% | 5446 |
| chr1 | 63185 | 0.03% | 266 |
| chr1_KI270712v1_random | 160 | 0.09% | 1 |
| chr2 | 78296 | 0.03% | 334 |
| chr3 | 54598 | 0.03% | 241 |
| chr4 | 64479 | 0.03% | 296 |
| chr4_GL000008v2_random | 1766 | 0.84% | 4 |
| chr5 | 84489 | 0.05% | 373 |
| chr6 | 52611 | 0.03% | 222 |
| chr7 | 78516 | 0.05% | 312 |
| chr8 | 65150 | 0.04% | 266 |
| chr9 | 42437 | 0.03% | 186 |
| chr10 | 46475 | 0.03% | 207 |
| chr11 | 38933 | 0.03% | 163 |
| chr12 | 69057 | 0.05% | 248 |
| chr13 | 51909 | 0.05% | 247 |
| chr14 | 30472 | 0.03% | 144 |
| chr14_GL000225v1_random | 166 | 0.08% | 1 |
| chr14_KI270722v1_random | 140 | 0.07% | 1 |
| chr15 | 41332 | 0.04% | 160 |
| chr16 | 33668 | 0.04% | 121 |
| chr17 | 24204 | 0.03% | 100 |
| chr17_GL000205v2_random | 2982 | 1.61% | 10 |
| chr17_KI270729v1_random | 857 | 0.31% | 3 |
| chr18 | 36753 | 0.05% | 159 |
| chr19 | 257099 | 0.44% | 847 |
| chr20 | 17686 | 0.03% | 75 |
| chr21 | 43150 | 0.09% | 196 |
| chr22 | 13140 | 0.03% | 55 |
| chr22_KI270732v1_random | 216 | 0.52% | 1 |
| chr22_KI270733v1_random | 309 | 0.17% | 2 |
| chr22_KI270735v1_random | 158 | 0.37% | 1 |
| chr22_KI270736v1_random | 3978 | 2.19% | 15 |
| chrUn_GL000214v1 | 250 | 0.18% | 1 |
| chrUn_GL000219v1 | 441 | 0.25% | 2 |
| chrUn_GL000220v1 | 236 | 0.15% | 1 |
| chrUn_GL000224v1 | 937 | 0.52% | 4 |
| chrUn_KI270333v1 | 217 | 8.04% | 1 |
| chrUn_KI270438v1 | 493 | 0.44% | 2 |
| chrUn_KI270442v1 | 3331 | 0.85% | 13 |
| chrUn_KI270465v1 | 232 | 13.08% | 1 |
| chrUn_KI270467v1 | 431 | 10.99% | 1 |
| chrUn_KI270515v1 | 221 | 3.47% | 1 |
| chrUn_KI270519v1 | 163 | 0.12% | 1 |
| chrUn_KI270589v1 | 614 | 1.38% | 3 |
| chrUn_KI270591v1 | 169 | 2.92% | 1 |
| chrUn_KI270744v1 | 259 | 0.15% | 1 |
| chrUn_KI270746v1 | 539 | 0.81% | 2 |
| chrUn_KI270750v1 | 163 | 0.11% | 1 |
| chrUn_KI270751v1 | 356 | 0.24% | 2 |
| chrUn_KI270757v1 | 692 | 0.97% | 3 |
| chrX | 30573 | 0.02% | 139 |
| chrY | 2456 | <0.01% | 9 |
| 3314 contigs with no values (125401706 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 5446 | 140 | 2138 | 246.26 | 205 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF257VHT.bed.gz | 92.5 KB | 05a41f0748065d9d134bb8a3ceecb823 |
| ENCFF257VHT.tabix.bed.gz | 51.91 KB | 7fa68b9edfedd73002fb415075f46338 |
| ENCFF257VHT.tabix.bed.gz.tbi | 45.29 KB | 00ec2201d7d540536cd3bd648d982359 |
| genomic_resource.yaml | 3.8 KB | 86f0c4a2b51f06d6f5039162b498ef32 |
| statistics/ |