Resource
| Id | Histone_ChIP-seq/ENCSR197XDQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR197XDQ [biosample_summary="Homo sapiens MCF-7" and target="H3F3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN239WKA|/analyses/ENCAN239WKA/} has in progress subobject document {a7fa7cec-df17-4b7d-8e31-50118d958736|/documents/a7fa7cec-df17-4b7d-8e31-50118d958736/} audit_internal_action: Released analysis {ENCAN239WKA|/analyses/ENCAN239WKA/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF183HME|/files/ENCFF183HME/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 32569135 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 {ENCFF626ORM|/files/ENCFF626ORM/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 22407444 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 {ENCFF626ORM|/files/ENCFF626ORM/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF626ORM|/files/ENCFF626ORM/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR197XDQ | float |
Histone_ChIP-seq_ENCSR197XDQ |
Histone_ChIP-seq ENCSR197XDQ [biosample_summary="Homo sapiens MCF-7" and target="H3F3A"]
|
 |
[1.29, 8.37] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7360844 | 0.23% | 14411 |
| chr1 | 500520 | 0.20% | 1010 |
| chr2 | 377522 | 0.16% | 842 |
| chr3 | 373676 | 0.19% | 742 |
| chr4 | 85483 | 0.04% | 197 |
| chr5 | 305420 | 0.17% | 632 |
| chr6 | 273589 | 0.16% | 601 |
| chr7 | 358542 | 0.23% | 747 |
| chr8 | 342879 | 0.24% | 659 |
| chr9 | 336040 | 0.24% | 662 |
| chr10 | 249124 | 0.19% | 542 |
| chr11 | 356340 | 0.26% | 681 |
| chr12 | 368672 | 0.28% | 751 |
| chr13 | 56032 | 0.05% | 120 |
| chr14 | 376696 | 0.35% | 770 |
| chr15 | 305674 | 0.30% | 612 |
| chr16 | 435875 | 0.48% | 867 |
| chr17 | 794171 | 0.95% | 1447 |
| chr18 | 23446 | 0.03% | 54 |
| chr19 | 335293 | 0.57% | 686 |
| chr20 | 916303 | 1.42% | 1402 |
| chr21 | 124877 | 0.27% | 241 |
| chr22 | 32160 | 0.06% | 74 |
| chrX | 32510 | 0.02% | 72 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 14411 | 178 | 4120 | 510.78 | 439 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF595UXF.bed.gz | 334.45 KB | bf3cf96b9be05097fffdf0275b046ab1 |
| ENCFF595UXF.tabix.bed.gz | 154.53 KB | 488c51fa1812453a5c1f9f96e317854a |
| ENCFF595UXF.tabix.bed.gz.tbi | 83.25 KB | 4b6e7aecfa4e17899e27e963cea20dde |
| genomic_resource.yaml | 3.92 KB | d8fb97b42e1b40fe1cee18edc1c84663 |
| statistics/ |