Resource
| Id | Histone_ChIP-seq/ENCSR771QCM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR771QCM [biosample_summary="Homo sapiens SU-DHL-6" and target="H3F3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN669QQW|/analyses/ENCAN669QQW/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF033JLT|/files/ENCFF033JLT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 23560132 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_not_compliant: Processed alignments file {ENCFF559HLS|/files/ENCFF559HLS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20740621 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 {ENCFF033JLT|/files/ENCFF033JLT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF033JLT|/files/ENCFF033JLT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR771QCM | float |
Histone_ChIP-seq_ENCSR771QCM |
Histone_ChIP-seq ENCSR771QCM [biosample_summary="Homo sapiens SU-DHL-6" and target="H3F3A"]
|
 |
[1.64, 15.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42874699 | 1.33% | 58096 |
| chr1 | 4244484 | 1.70% | 5886 |
| chr2 | 3747456 | 1.55% | 5123 |
| chr3 | 2965936 | 1.50% | 3915 |
| chr4 | 1470787 | 0.77% | 2062 |
| chr5 | 2127190 | 1.17% | 2991 |
| chr6 | 3091461 | 1.81% | 3949 |
| chr7 | 2373101 | 1.49% | 3071 |
| chr8 | 2025607 | 1.40% | 2565 |
| chr9 | 1747531 | 1.26% | 2273 |
| chr10 | 1949186 | 1.46% | 2610 |
| chr11 | 1975636 | 1.46% | 2532 |
| chr12 | 2252894 | 1.69% | 3174 |
| chr13 | 1087614 | 0.95% | 1447 |
| chr14 | 1544277 | 1.44% | 2133 |
| chr15 | 1604041 | 1.57% | 2217 |
| chr16 | 1287829 | 1.43% | 1885 |
| chr17 | 2001159 | 2.40% | 2811 |
| chr17_KI270729v1_random | 3997 | 1.42% | 7 |
| chr18 | 760787 | 0.95% | 1070 |
| chr19 | 1523643 | 2.60% | 2266 |
| chr20 | 1280698 | 1.99% | 1635 |
| chr21 | 441652 | 0.95% | 599 |
| chr22 | 732074 | 1.44% | 982 |
| chrUn_GL000216v2 | 245 | 0.14% | 1 |
| chrUn_KI270466v1 | 646 | 52.39% | 1 |
| chrUn_KI270467v1 | 1602 | 40.87% | 1 |
| chrX | 633166 | 0.41% | 890 |
| 3339 contigs with no values (185841900 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 58096 | 195 | 16698 | 738 | 539 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF046FWB.bed.gz | 1.33 MB | 002d4ffa74fc065901d0c7ecec16f271 |
| ENCFF046FWB.tabix.bed.gz | 614.79 KB | 8706aa9eb665709e69e2dea72c2f7af7 |
| ENCFF046FWB.tabix.bed.gz.tbi | 155.55 KB | 200bc33b2f585288ae066818bcb9c4c7 |
| genomic_resource.yaml | 3.77 KB | ab352ce0f2c749f1207ef21d3197a7e2 |
| statistics/ |