Resource
| Id | Histone_ChIP-seq/ENCSR351SZH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR351SZH [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN253JXE|/analyses/ENCAN253JXE/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF660XBY|/files/ENCFF660XBY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 20479157 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 redacted alignments file {ENCFF660XBY|/files/ENCFF660XBY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 redacted alignments file {ENCFF660XBY|/files/ENCFF660XBY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.18. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR351SZH | float |
Histone_ChIP-seq_ENCSR351SZH |
Histone_ChIP-seq ENCSR351SZH [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell" and target="H3K4me1"]
|
 |
[1.83, 24.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 74774456 | 2.32% | 71862 |
| chr1 | 7627874 | 3.06% | 7170 |
| chr2 | 6395603 | 2.64% | 6000 |
| chr3 | 4719204 | 2.38% | 4612 |
| chr4 | 2504444 | 1.32% | 2610 |
| chr5 | 3666253 | 2.02% | 3520 |
| chr6 | 4503661 | 2.64% | 4465 |
| chr7 | 3286132 | 2.06% | 3246 |
| chr8 | 2870417 | 1.98% | 2877 |
| chr9 | 2857316 | 2.06% | 2722 |
| chr10 | 3476693 | 2.60% | 3325 |
| chr11 | 3892931 | 2.88% | 3535 |
| chr12 | 3892796 | 2.92% | 3859 |
| chr13 | 1772645 | 1.55% | 1741 |
| chr14 | 2995444 | 2.80% | 2690 |
| chr15 | 2527807 | 2.48% | 2422 |
| chr16 | 2705564 | 2.99% | 2568 |
| chr17 | 4308955 | 5.18% | 4024 |
| chr18 | 1216041 | 1.51% | 1189 |
| chr19 | 3161713 | 5.39% | 3156 |
| chr20 | 2046144 | 3.18% | 1949 |
| chr21 | 1022608 | 2.19% | 935 |
| chr22 | 1745891 | 3.44% | 1564 |
| chrX | 1475625 | 0.95% | 1571 |
| chrY | 102695 | 0.18% | 112 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 71862 | 225 | 21966 | 1040.53 | 771 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF269MSP.bed.gz | 1.58 MB | 883d2761507d377991d33690b0dc5fb6 |
| ENCFF269MSP.tabix.bed.gz | 752.59 KB | 70a564fe14e4b79ed17a1734f61d69c5 |
| ENCFF269MSP.tabix.bed.gz.tbi | 199.1 KB | c1fc4c97f96bed5c46128da5cf181d89 |
| genomic_resource.yaml | 3.37 KB | 737e11802dec74bfddbf8caf00251464 |
| statistics/ |