Resource
| Id | Histone_ChIP-seq/ENCSR225VCV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR225VCV [biosample_summary="Homo sapiens thyroid gland tissue male adult (37 years)" and target="H3K36me3"] |
| Description |
status: archived biological_replicates: Rep 1, Rep 2 summary: male adult (37 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN291EZU|/analyses/ENCAN291EZU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF772BIG|/files/ENCFF772BIG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17438125 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF772BIG|/files/ENCFF772BIG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF772BIG|/files/ENCFF772BIG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.98. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR225VCV | float |
Histone_ChIP-seq_ENCSR225VCV |
Histone_ChIP-seq ENCSR225VCV [biosample_summary="Homo sapiens thyroid gland tissue male adult (37 years)" and target="H3K36me3"]
|
 |
[1.47, 10.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30126058 | 0.94% | 56084 |
| chr1 | 3226525 | 1.30% | 5796 |
| chr2 | 2341551 | 0.97% | 4526 |
| chr3 | 1831386 | 0.92% | 3492 |
| chr4 | 1115026 | 0.59% | 2390 |
| chr5 | 1632746 | 0.90% | 3063 |
| chr6 | 1437731 | 0.84% | 2741 |
| chr7 | 1232521 | 0.77% | 2446 |
| chr8 | 1100424 | 0.76% | 2090 |
| chr9 | 1221457 | 0.88% | 2276 |
| chr10 | 1279052 | 0.96% | 2454 |
| chr11 | 1615800 | 1.20% | 2887 |
| chr12 | 1826248 | 1.37% | 3291 |
| chr13 | 553932 | 0.48% | 1201 |
| chr14 | 1170751 | 1.09% | 2206 |
| chr14_KI270725v1_random | 244 | 0.14% | 1 |
| chr15 | 1144793 | 1.12% | 2187 |
| chr16 | 1379366 | 1.53% | 2359 |
| chr17 | 1753719 | 2.11% | 3139 |
| chr17_GL000205v2_random | 256 | 0.14% | 1 |
| chr18 | 442656 | 0.55% | 883 |
| chr19 | 1907353 | 3.25% | 3052 |
| chr20 | 796875 | 1.24% | 1501 |
| chr21 | 285224 | 0.61% | 574 |
| chr22 | 709667 | 1.40% | 1249 |
| chrUn_GL000219v1 | 1029 | 0.57% | 2 |
| chrUn_GL000220v1 | 301 | 0.19% | 1 |
| chrUn_KI270333v1 | 740 | 27.42% | 3 |
| chrUn_KI270336v1 | 298 | 29.04% | 1 |
| chrUn_KI270337v1 | 640 | 57.09% | 1 |
| chrUn_KI270442v1 | 195 | 0.05% | 1 |
| chrUn_KI270466v1 | 969 | 78.59% | 1 |
| chrUn_KI270467v1 | 1481 | 37.78% | 1 |
| chrX | 106283 | 0.07% | 250 |
| chrY | 8819 | 0.02% | 18 |
| 3332 contigs with no values (127975624 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56084 | 190 | 12807 | 537.16 | 397 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF487XSW.bed.gz | 1.04 MB | 6990952d13c4a965d1dfd705d69555f3 |
| ENCFF487XSW.tabix.bed.gz | 558.5 KB | 7994e87ae42c7ba9109386ecc1e90767 |
| ENCFF487XSW.tabix.bed.gz.tbi | 123.75 KB | 7b48bffb9495b24a41510c2abf58284c |
| genomic_resource.yaml | 3.24 KB | 8de0c338d82cf7114f3c3a1409f5b496 |
| statistics/ |