Resource
| Id | Histone_ChIP-seq/ENCSR180AAB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR180AAB [biosample_summary="Homo sapiens PC-9" and target="H3F3A"] |
| Description |
status: archived biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN341FIH|/analyses/ENCAN341FIH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF763ZGF|/files/ENCFF763ZGF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19538231 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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: Processed alignments file {ENCFF792YEO|/files/ENCFF792YEO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 39505078 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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 {ENCFF763ZGF|/files/ENCFF763ZGF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF763ZGF|/files/ENCFF763ZGF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.00. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR180AAB | float |
Histone_ChIP-seq_ENCSR180AAB |
Histone_ChIP-seq ENCSR180AAB [biosample_summary="Homo sapiens PC-9" and target="H3F3A"]
|
 |
[1.5, 13.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 103936536 | 3.23% | 122497 |
| chr1 | 10852960 | 4.36% | 12595 |
| chr1_KI270713v1_random | 2481 | 6.09% | 4 |
| chr2 | 8638260 | 3.57% | 10210 |
| chr3 | 6636307 | 3.35% | 7741 |
| chr4 | 2412267 | 1.27% | 3111 |
| chr5 | 5083383 | 2.80% | 6219 |
| chr6 | 5447818 | 3.19% | 6502 |
| chr7 | 5910561 | 3.71% | 6995 |
| chr8 | 4178384 | 2.88% | 4764 |
| chr9 | 3756340 | 2.71% | 4589 |
| chr10 | 3715176 | 2.78% | 4397 |
| chr11 | 6174660 | 4.57% | 6999 |
| chr12 | 5464885 | 4.10% | 6455 |
| chr13 | 2100820 | 1.84% | 2690 |
| chr14 | 3541936 | 3.31% | 4046 |
| chr15 | 2693712 | 2.64% | 3219 |
| chr16 | 4265990 | 4.72% | 5152 |
| chr17 | 6235803 | 7.49% | 7304 |
| chr17_GL000205v2_random | 1364 | 0.73% | 1 |
| chr18 | 1690102 | 2.10% | 2042 |
| chr19 | 5526843 | 9.43% | 6485 |
| chr20 | 4163213 | 6.46% | 4502 |
| chr21 | 692462 | 1.48% | 842 |
| chr22 | 3112819 | 6.13% | 3483 |
| chr22_KI270733v1_random | 1403 | 0.78% | 4 |
| chrUn_GL000220v1 | 688 | 0.43% | 2 |
| chrUn_KI270442v1 | 373 | 0.10% | 1 |
| chrUn_KI270467v1 | 1043 | 26.61% | 2 |
| chrUn_KI270742v1 | 298 | 0.16% | 1 |
| chrUn_KI270749v1 | 798 | 0.50% | 1 |
| chrX | 1633387 | 1.05% | 2139 |
| 3335 contigs with no values (184995111 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 122497 | 190 | 35823 | 848.48 | 614 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF926ZHI.bed.gz | 2.91 MB | d55123468d632b4f281d6bf3cfa982fb |
| ENCFF926ZHI.tabix.bed.gz | 1.27 MB | 67f58c19ff98535a0c4734a2edd860af |
| ENCFF926ZHI.tabix.bed.gz.tbi | 274.69 KB | f97e75c5ddf72c1719b3610ddae70452 |
| genomic_resource.yaml | 3.65 KB | bdb3559fe2d7eaac04aab27ef1fc47bc |
| statistics/ |