Resource
| Id | Histone_ChIP-seq/ENCSR153SGD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR153SGD [biosample_summary="Homo sapiens HUES48" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN820RTF|/analyses/ENCAN820RTF/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF270NKU|/files/ENCFF270NKU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18210503 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF270NKU|/files/ENCFF270NKU/} processed by ChIP-seq ENCODE3 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 alignments file {ENCFF270NKU|/files/ENCFF270NKU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.60. 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 {ENCFF443UEL|/files/ENCFF443UEL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF443UEL|/files/ENCFF443UEL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.47. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR153SGD | float |
Histone_ChIP-seq_ENCSR153SGD |
Histone_ChIP-seq ENCSR153SGD [biosample_summary="Homo sapiens HUES48" and target="H3K4me3"]
|
 |
[1.7, 81.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 55465209 | 1.72% | 44181 |
| chr1 | 5262229 | 2.11% | 4077 |
| chr1_KI270709v1_random | 1130 | 1.69% | 3 |
| chr1_KI270713v1_random | 2863 | 7.03% | 5 |
| chr2 | 3828437 | 1.58% | 3056 |
| chr2_KI270716v1_random | 376 | 0.24% | 1 |
| chr3 | 3122141 | 1.57% | 2419 |
| chr4 | 2468481 | 1.30% | 1982 |
| chr4_GL000008v2_random | 2699 | 1.29% | 3 |
| chr5 | 2837227 | 1.56% | 2212 |
| chr6 | 3477909 | 2.04% | 2522 |
| chr7 | 2727100 | 1.71% | 2252 |
| chr8 | 2195224 | 1.51% | 1774 |
| chr9 | 2193429 | 1.58% | 1733 |
| chr10 | 2357357 | 1.76% | 1912 |
| chr11 | 2852536 | 2.11% | 2202 |
| chr12 | 2846342 | 2.14% | 2134 |
| chr13 | 1271971 | 1.11% | 1022 |
| chr14 | 1797642 | 1.68% | 1363 |
| chr14_GL000225v1_random | 4564 | 2.16% | 10 |
| chr14_KI270725v1_random | 425 | 0.25% | 1 |
| chr15 | 1757994 | 1.72% | 1387 |
| chr16 | 1943496 | 2.15% | 1587 |
| chr17 | 2798540 | 3.36% | 2181 |
| chr17_GL000205v2_random | 10170 | 5.48% | 18 |
| chr17_KI270729v1_random | 23559 | 8.39% | 31 |
| chr17_KI270730v1_random | 547 | 0.49% | 1 |
| chr18 | 1053138 | 1.31% | 850 |
| chr19 | 3206491 | 5.47% | 2741 |
| chr20 | 1449490 | 2.25% | 1193 |
| chr21 | 564843 | 1.21% | 514 |
| chr22 | 1025299 | 2.02% | 864 |
| chr22_KI270733v1_random | 589 | 0.33% | 2 |
| chr22_KI270735v1_random | 793 | 1.85% | 2 |
| chr22_KI270736v1_random | 10170 | 5.59% | 18 |
| chr22_KI270738v1_random | 386 | 0.39% | 1 |
| chrUn_GL000195v1 | 885 | 0.48% | 3 |
| chrUn_GL000216v2 | 27143 | 15.37% | 36 |
| chrUn_GL000219v1 | 1543 | 0.86% | 3 |
| chrUn_GL000220v1 | 331 | 0.20% | 1 |
| chrUn_GL000224v1 | 366 | 0.20% | 1 |
| chrUn_KI270333v1 | 288 | 10.67% | 1 |
| chrUn_KI270438v1 | 6416 | 5.70% | 15 |
| chrUn_KI270442v1 | 19605 | 5.00% | 35 |
| chrUn_KI270466v1 | 1054 | 85.48% | 1 |
| chrUn_KI270467v1 | 1582 | 40.36% | 1 |
| chrUn_KI270515v1 | 302 | 4.75% | 1 |
| chrUn_KI270519v1 | 631 | 0.46% | 1 |
| chrUn_KI270538v1 | 537 | 0.59% | 1 |
| chrUn_KI270584v1 | 202 | 4.48% | 1 |
| chrUn_KI270589v1 | 1539 | 3.46% | 2 |
| chrUn_KI270744v1 | 1208 | 0.72% | 4 |
| chrUn_KI270746v1 | 1938 | 2.91% | 4 |
| chrUn_KI270749v1 | 591 | 0.37% | 1 |
| chrUn_KI270750v1 | 2431 | 1.63% | 6 |
| chrUn_KI270751v1 | 808 | 0.54% | 1 |
| chrUn_KI270757v1 | 382 | 0.54% | 1 |
| chrX | 2294513 | 1.47% | 1975 |
| chrY | 5327 | 0.01% | 13 |
| 3308 contigs with no values (124697172 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44181 | 185 | 13627 | 1255.41 | 829 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF530UOO.bed.gz | 1.18 MB | 99a0665b8cfc5200da21c894b6e66a8c |
| ENCFF530UOO.tabix.bed.gz | 504.49 KB | b72807d11b9823992b10074a7bc23477 |
| ENCFF530UOO.tabix.bed.gz.tbi | 223.8 KB | aeda9b12f6aee3f60e9a4935bd95a33c |
| genomic_resource.yaml | 4.46 KB | ec73b200347f507f2e90899bf766be85 |
| statistics/ |