Chromosomal Sex

XY

Median Read Length

346bp

Total Reads

180,183

Chromosome Copy Summary

0 copies 1 copies 2 copies 3 copies 4 copies
- X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 21 -

Ideoplot

Red: Increased copy number detected

Blue: Decreased copy number detected

Yellow: QDNASeq no call

Black: 'acen', 'gvar', or 'stalk'. Read counts of < -2 converted to 2

Detailed CNV Results

QDNASeq Smoothed Read Counts

Bin size 500Mb, No call not displayed

chr start end genes read count call
chr21 14000000 14500000 Genes 0.677 1
chr21 14500000 15000000 Genes 0.449 1
chr21 15000000 15500000 Genes 0.789 1
chr21 15500000 16000000 Genes 0.579 1
chr21 16000000 16500000 Genes 0.357 1
chr21 17000000 17500000 Genes 0.455 1
chr21 17500000 18000000 Genes 0.442 1
chr21 18000000 18500000 Genes 0.603 1
chr21 18500000 19000000 Genes 0.765 1
chr21 19000000 19500000 Genes -0.084 1
chr21 19500000 20000000 Genes 0.344 1
chr21 20000000 20500000 Genes 0.425 1
chr21 20500000 21000000 Genes 0.592 1
chr21 21000000 21500000 Genes 0.283 1
chr21 21500000 22000000 Genes 0.595 1
chr21 22000000 22500000 Genes 0.344 1
chr21 22500000 23000000 Genes 0.196 1
chr21 23000000 23500000 Genes 0.296 1
chr21 23500000 24000000 Genes 0.264 1
chr21 24000000 24500000 Genes 0.727 1
chr21 24500000 25000000 Genes 1.047 1
chr21 25000000 25500000 Genes 0.237 1
chr21 25500000 26000000 Genes 0.88 1
chr21 26000000 26500000 Genes 0.639 1
chr21 26500000 27000000 Genes 0.525 1
chr21 27000000 27500000 Genes 0.81 1
chr21 27500000 28000000 Genes 0.635 1
chr21 28000000 28500000 Genes 0.363 1
chr21 28500000 29000000 Genes 0.912 1
chr21 29000000 29500000 Genes 0.973 1
chr21 29500000 30000000 Genes 0.474 1
chr21 30000000 30500000 Genes 0.841 1
chr21 30500000 31000000 Genes 0.684 1
chr21 31000000 31500000 Genes 0.713 1
chr21 31500000 32000000 Genes 0.66 1
chr21 32500000 33000000 Genes 0.868 1
chr21 33000000 33500000 Genes 0.216 1
chr21 33500000 34000000 Genes 0.712 1
chr21 34000000 34500000 Genes 0.454 1
chr21 34500000 35000000 Genes 0.318 1
chr21 35000000 35500000 Genes 0.664 1
chr21 36000000 36500000 Genes 0.479 1
chr21 36500000 37000000 Genes 0.472 1
chr21 37000000 37500000 Genes 0.672 1
chr21 37500000 38000000 Genes 0.764 1
chr21 38000000 38500000 Genes 1.091 1
chr21 38500000 39000000 Genes 0.748 1
chr21 39000000 39500000 Genes 0.41 1
chr21 39500000 40000000 Genes 0.389 1
chr21 40000000 40500000 Genes 0.135 1
chr21 40500000 41000000 Genes 0.681 1
chr21 41000000 41500000 Genes 0.461 1
chr21 41500000 42000000 Genes 0.599 1
chr21 42000000 42500000 Genes 0.667 1
chr21 42500000 43000000 Genes 0.851 1
chr21 43500000 44000000 Genes 0.323 1
chr21 44500000 45000000 Genes 0.942 1
chr21 45500000 46000000 Genes 0.159 1
chr21 46000000 46500000 Genes 0.221 1
chr21 46500000 46709983 Genes 0.569 1
chrX 0 500000 Genes 0.342 -1
chrX 500000 1000000 Genes -0.207 -1
chrX 1000000 1500000 Genes -0.242 -1
chrX 1500000 2000000 Genes 0.419 -1
chrX 2000000 2500000 Genes 0.397 -1
chrX 2500000 3000000 Genes -0.137 -1
chrX 3000000 3500000 Genes -0.105 -1
chrX 3500000 4000000 Genes -0.917 -1
chrX 4500000 5000000 Genes -1.024 -1
chrX 5500000 6000000 Genes -0.95 -1
chrX 6000000 6500000 Genes -0.605 -1
chrX 6500000 7000000 Genes -1.48 -1
chrX 7000000 7500000 Genes -0.804 -1
chrX 7500000 8000000 Genes -0.999 -1
chrX 8000000 8500000 Genes -0.299 -1
chrX 8500000 9000000 Genes -0.895 -1
chrX 9000000 9500000 Genes -0.779 -1
chrX 9500000 10000000 Genes -1.156 -1
chrX 10000000 10500000 Genes -1.469 -1
chrX 10500000 11000000 Genes -1.123 -1
chrX 11000000 11500000 Genes -0.776 -1
chrX 11500000 12000000 Genes -1.38 -1
chrX 12000000 12500000 Genes -0.712 -1
chrX 12500000 13000000 Genes -0.23 -1
chrX 13000000 13500000 Genes -1.247 -1
chrX 13500000 14000000 Genes -1.482 -1
chrX 14000000 14500000 Genes -0.099 -1
chrX 14500000 15000000 Genes -0.816 -1
chrX 15000000 15500000 Genes -1.853 -1
chrX 16000000 16500000 Genes -0.376 -1
chrX 16500000 17000000 Genes -1.33 -1
chrX 17500000 18000000 Genes -0.559 -1
chrX 18000000 18500000 Genes -1.146 -1
chrX 18500000 19000000 Genes -1.394 -1
chrX 19000000 19500000 Genes -1.241 -1
chrX 19500000 20000000 Genes -0.731 -1
chrX 20000000 20500000 Genes -0.832 -1
chrX 20500000 21000000 Genes -0.876 -1
chrX 21000000 21500000 Genes -0.123 -1
chrX 21500000 22000000 Genes -0.853 -1
chrX 22000000 22500000 Genes -1.25 -1
chrX 22500000 23000000 Genes -1.02 -1
chrX 23000000 23500000 Genes -0.806 -1
chrX 23500000 24000000 Genes -1.002 -1
chrX 24500000 25000000 Genes -0.761 -1
chrX 25000000 25500000 Genes -0.961 -1
chrX 25500000 26000000 Genes -0.814 -1
chrX 26000000 26500000 Genes -0.752 -1
chrX 26500000 27000000 Genes -0.214 -1
chrX 27000000 27500000 Genes -1.6 -1
chrX 27500000 28000000 Genes -2.242 -1
chrX 28000000 28500000 Genes -1.755 -1
chrX 28500000 29000000 Genes -1.629 -1
chrX 29000000 29500000 Genes -0.563 -1
chrX 29500000 30000000 Genes -0.811 -1
chrX 30000000 30500000 Genes -1.238 -1
chrX 30500000 31000000 Genes -0.994 -1
chrX 31000000 31500000 Genes -0.591 -1
chrX 31500000 32000000 Genes -1.123 -1
chrX 32000000 32500000 Genes -0.809 -1
chrX 32500000 33000000 Genes -1.123 -1
chrX 33000000 33500000 Genes -0.724 -1
chrX 34000000 34500000 Genes -0.683 -1
chrX 34500000 35000000 Genes -1.111 -1
chrX 35000000 35500000 Genes -1.354 -1
chrX 35500000 36000000 Genes -0.537 -1
chrX 36000000 36500000 Genes -1.07 -1
chrX 36500000 37000000 Genes -0.26 -1
chrX 37000000 37500000 Genes -0.717 -1
chrX 37500000 38000000 Genes -1.772 -1
chrX 38000000 38500000 Genes -1.173 -1
chrX 38500000 39000000 Genes -0.621 -1
chrX 39000000 39500000 Genes -1.09 -1
chrX 39500000 40000000 Genes -0.679 -1
chrX 40000000 40500000 Genes -0.77 -1
chrX 40500000 41000000 Genes -1.016 -1
chrX 41000000 41500000 Genes -0.899 -1
chrX 41500000 42000000 Genes -0.999 -1
chrX 42000000 42500000 Genes -0.806 -1
chrX 42500000 43000000 Genes -1.099 -1
chrX 43000000 43500000 Genes -0.744 -1
chrX 43500000 44000000 Genes -0.747 -1
chrX 44000000 44500000 Genes -1.359 -1
chrX 44500000 45000000 Genes -0.599 -1
chrX 45000000 45500000 Genes -0.575 -1
chrX 45500000 46000000 Genes -1.041 -1
chrX 46000000 46500000 Genes -1.352 -1
chrX 46500000 47000000 Genes -1.016 -1
chrX 47000000 47500000 Genes 0.055 -1
chrX 47500000 48000000 Genes -0.794 -1
chrX 48000000 48500000 Genes 0.166 -1
chrX 48500000 49000000 Genes -0.57 -1
chrX 49000000 49500000 Genes -1.559 -1
chrX 49500000 50000000 Genes -0.585 -1
chrX 50000000 50500000 Genes -0.632 -1
chrX 50500000 51000000 Genes -1.274 -1
chrX 51000000 51500000 Genes -0.689 -1
chrX 51500000 52000000 Genes -1.336 -1
chrX 52000000 52500000 Genes -2.213 -1
chrX 52500000 53000000 Genes -0.742 -1
chrX 53000000 53500000 Genes -0.637 -1
chrX 53500000 54000000 Genes -1.45 -1
chrX 54000000 54500000 Genes -1.116 -1
chrX 54500000 55000000 Genes -0.223 -1
chrX 55500000 56000000 Genes -0.173 -1
chrX 56000000 56500000 Genes -0.494 -1
chrX 56500000 57000000 Genes -0.788 -1
chrX 57000000 57500000 Genes -1.327 -1
chrX 57500000 58000000 Genes -1.164 -1
chrX 63000000 63500000 Genes -1.774 -1
chrX 63500000 64000000 Genes -0.689 -1
chrX 64000000 64500000 Genes 0.046 -1
chrX 64500000 65000000 Genes -1.641 -1
chrX 65000000 65500000 Genes -0.628 -1
chrX 65500000 66000000 Genes -1.015 -1
chrX 66000000 66500000 Genes -0.61 -1
chrX 66500000 67000000 Genes -0.863 -1
chrX 67000000 67500000 Genes -0.344 -1
chrX 67500000 68000000 Genes -1.422 -1
chrX 68000000 68500000 Genes -0.722 -1
chrX 68500000 69000000 Genes -0.26 -1
chrX 69000000 69500000 Genes -0.345 -1
chrX 69500000 70000000 Genes -0.4 -1
chrX 70500000 71000000 Genes -1.31 -1
chrX 71000000 71500000 Genes -1.625 -1
chrX 71500000 72000000 Genes -1.544 -1
chrX 72000000 72500000 Genes -0.898 -1
chrX 72500000 73000000 Genes -2.492 -1
chrX 73000000 73500000 Genes -1.285 -1
chrX 73500000 74000000 Genes -2.056 -1
chrX 74000000 74500000 Genes -0.23 -1
chrX 74500000 75000000 Genes -0.645 -1
chrX 75000000 75500000 Genes -0.842 -1
chrX 75500000 76000000 Genes -0.35 -1
chrX 76000000 76500000 Genes -1.292 -1
chrX 76500000 77000000 Genes -0.428 -1
chrX 77000000 77500000 Genes -1.425 -1
chrX 78000000 78500000 Genes -0.849 -1
chrX 79000000 79500000 Genes -1.129 -1
chrX 79500000 80000000 Genes -1.025 -1
chrX 80000000 80500000 Genes -0.783 -1
chrX 80500000 81000000 Genes -1.502 -1
chrX 81000000 81500000 Genes -1.002 -1
chrX 81500000 82000000 Genes -0.605 -1
chrX 82000000 82500000 Genes -1.463 -1
chrX 82500000 83000000 Genes -0.919 -1
chrX 83000000 83500000 Genes -0.906 -1
chrX 83500000 84000000 Genes -0.796 -1
chrX 84500000 85000000 Genes -0.321 -1
chrX 85000000 85500000 Genes -1.752 -1
chrX 85500000 86000000 Genes -1.128 -1
chrX 86000000 86500000 Genes -0.726 -1
chrX 86500000 87000000 Genes -0.378 -1
chrX 87000000 87500000 Genes -1.281 -1
chrX 87500000 88000000 Genes -0.74 -1
chrX 88000000 88500000 Genes -1.433 -1
chrX 88500000 89000000 Genes -1.17 -1
chrX 89000000 89500000 Genes -1.803 -1
chrX 89500000 90000000 Genes -2.594 -1
chrX 90000000 90500000 Genes -2.006 -1
chrX 91000000 91500000 Genes -1.06 -1
chrX 92000000 92500000 Genes -1.589 -1
chrX 93000000 93500000 Genes -0.851 -1
chrX 93500000 94000000 Genes -1.325 -1
chrX 94000000 94500000 Genes -0.551 -1
chrX 94500000 95000000 Genes -1.04 -1
chrX 95000000 95500000 Genes -0.497 -1
chrX 95500000 96000000 Genes -0.963 -1
chrX 96000000 96500000 Genes -0.906 -1
chrX 96500000 97000000 Genes -1.307 -1
chrX 97000000 97500000 Genes -0.783 -1
chrX 97500000 98000000 Genes -1.009 -1
chrX 98000000 98500000 Genes -0.695 -1
chrX 98500000 99000000 Genes -1.155 -1
chrX 99000000 99500000 Genes -1.098 -1
chrX 99500000 100000000 Genes -0.433 -1
chrX 100500000 101000000 Genes -0.476 -1
chrX 101000000 101500000 Genes -0.4 -1
chrX 101500000 102000000 Genes -1.089 -1
chrX 103000000 103500000 Genes -1.722 -1
chrX 103500000 104000000 Genes -0.8 -1
chrX 104500000 105000000 Genes -1.251 -1
chrX 105000000 105500000 Genes -0.535 -1
chrX 105500000 106000000 Genes -0.579 -1
chrX 106500000 107000000 Genes -1.357 -1
chrX 107000000 107500000 Genes -0.994 -1
chrX 107500000 108000000 Genes -0.977 -1
chrX 108000000 108500000 Genes -1.859 -1
chrX 108500000 109000000 Genes -0.726 -1
chrX 109000000 109500000 Genes -0.292 -1
chrX 109500000 110000000 Genes -1.053 -1
chrX 110000000 110500000 Genes -0.6 -1
chrX 110500000 111000000 Genes -1.159 -1
chrX 111500000 112000000 Genes -1.057 -1
chrX 112000000 112500000 Genes -0.981 -1
chrX 112500000 113000000 Genes -1.294 -1
chrX 113000000 113500000 Genes -0.266 -1
chrX 113500000 114000000 Genes -1.098 -1
chrX 114000000 114500000 Genes -0.588 -1
chrX 114500000 115000000 Genes -0.833 -1
chrX 115000000 115500000 Genes -0.584 -1
chrX 115500000 116000000 Genes -2.099 -1
chrX 116000000 116500000 Genes -0.404 -1
chrX 116500000 117000000 Genes -0.693 -1
chrX 117000000 117500000 Genes -1.141 -1
chrX 117500000 118000000 Genes -0.918 -1
chrX 118000000 118500000 Genes -0.635 -1
chrX 118500000 119000000 Genes -1.409 -1
chrX 119000000 119500000 Genes -1.211 -1
chrX 119500000 120000000 Genes -0.668 -1
chrX 120000000 120500000 Genes -0.919 -1
chrX 120500000 121000000 Genes -1.247 -1
chrX 121000000 121500000 Genes -1.082 -1
chrX 121500000 122000000 Genes -1.448 -1
chrX 122000000 122500000 Genes -0.726 -1
chrX 122500000 123000000 Genes -1.098 -1
chrX 123000000 123500000 Genes -0.853 -1
chrX 123500000 124000000 Genes -1.176 -1
chrX 124000000 124500000 Genes -1.347 -1
chrX 124500000 125000000 Genes -0.943 -1
chrX 125000000 125500000 Genes -1.127 -1
chrX 125500000 126000000 Genes -1.281 -1
chrX 127000000 127500000 Genes -0.703 -1
chrX 127500000 128000000 Genes -2.145 -1
chrX 128000000 128500000 Genes -0.311 -1
chrX 128500000 129000000 Genes -1.461 -1
chrX 129000000 129500000 Genes -1.028 -1
chrX 130000000 130500000 Genes -0.962 -1
chrX 130500000 131000000 Genes -0.683 -1
chrX 131000000 131500000 Genes -1.204 -1
chrX 131500000 132000000 Genes -0.61 -1
chrX 132000000 132500000 Genes -1.636 -1
chrX 132500000 133000000 Genes -1.4 -1
chrX 133500000 134000000 Genes -0.526 -1
chrX 134000000 134500000 Genes -1.137 -1
chrX 134500000 135000000 Genes -0.84 -1
chrX 135500000 136000000 Genes -0.696 -1
chrX 136000000 136500000 Genes -1.012 -1
chrX 136500000 137000000 Genes -0.378 -1
chrX 137000000 137500000 Genes -0.912 -1
chrX 137500000 138000000 Genes -0.583 -1
chrX 138000000 138500000 Genes -0.945 -1
chrX 138500000 139000000 Genes -0.662 -1
chrX 139000000 139500000 Genes -0.541 -1
chrX 139500000 140000000 Genes -0.965 -1
chrX 140000000 140500000 Genes -0.832 -1
chrX 140500000 141000000 Genes -1.118 -1
chrX 141000000 141500000 Genes -1.114 -1
chrX 141500000 142000000 Genes -1.183 -1
chrX 142000000 142500000 Genes -0.846 -1
chrX 142500000 143000000 Genes -1.613 -1
chrX 144000000 144500000 Genes -2.18 -1
chrX 144500000 145000000 Genes -0.85 -1
chrX 145000000 145500000 Genes -0.368 -1
chrX 145500000 146000000 Genes -1.166 -1
chrX 146000000 146500000 Genes -1.131 -1
chrX 147000000 147500000 Genes -1.307 -1
chrX 147500000 148000000 Genes -0.758 -1
chrX 148000000 148500000 Genes -0.772 -1
chrX 148500000 149000000 Genes -0.982 -1
chrX 149000000 149500000 Genes -1.462 -1
chrX 149500000 150000000 Genes -0.811 -1
chrX 150000000 150500000 Genes -0.524 -1
chrX 150500000 151000000 Genes -1.156 -1
chrX 151000000 151500000 Genes -0.666 -1
chrX 151500000 152000000 Genes -0.45 -1
chrX 152000000 152500000 Genes -0.36 -1
chrX 152500000 153000000 Genes -0.705 -1
chrX 153000000 153500000 Genes -1.375 -1
chrX 153500000 154000000 Genes -1.026 -1
chrX 154000000 154500000 Genes -1.684 -1
chrX 154500000 155000000 Genes -1.064 -1
chrX 155000000 155500000 Genes -0.717 -1
chrX 155500000 156000000 Genes -0.59 -1
chrY 2500000 3000000 Genes -1.364 -1
chrY 3000000 3500000 Genes -1.419 -1
chrY 3500000 4000000 Genes -2.007 -1
chrY 6500000 7000000 Genes -0.874 -1
chrY 7000000 7500000 Genes -0.576 -1
chrY 7500000 8000000 Genes -1.215 -1
chrY 8000000 8500000 Genes -1.406 -1
chrY 8500000 9000000 Genes -0.706 -1
chrY 9500000 10000000 Genes -1.713 -1
chrY 12000000 12500000 Genes -0.875 -1
chrY 12500000 13000000 Genes -1.298 -1
chrY 13000000 13500000 Genes -0.739 -1
chrY 13500000 14000000 Genes -1.136 -1
chrY 14000000 14500000 Genes -1.099 -1
chrY 14500000 15000000 Genes -0.403 -1
chrY 15000000 15500000 Genes -1.022 -1
chrY 15500000 16000000 Genes -0.77 -1
chrY 16000000 16500000 Genes -2.009 -1
chrY 16500000 17000000 Genes -0.713 -1
chrY 17000000 17500000 Genes -0.711 -1
chrY 18500000 19000000 Genes -1.973 -1
chrY 19000000 19500000 Genes -1.542 -1
chrY 19500000 20000000 Genes -0.583 -1
chrY 20500000 21000000 Genes -0.712 -1
chrY 21000000 21500000 Genes -1.081 -1
chrY 26500000 27000000 Genes -0.106 -1

Quality Control Data

Histogram of Read Lengths

N.B. The read length affects the results of QDNASeq analysis. In future versions we will provide preset parameters based on detected read length

QDNASeq Copy Number QC Plots
Median read counts per genomic bin shown as a function of GC content and mappability Read count relationship between sequence depth and noise

Software versions

Name Version
pysam 0.20.0
R 4.2.2
QDNAseq 1.34.0
samtools 1.16.1

Workflow parameters

Key Value
help False
version False
disable_ping False
threads 4
aws_image_prefix None
aws_queue None
out_dir wf-human-variation
process_label wfdefault
snp False
sv False
methyl False
mapula False
cnv True
sv_benchmark False
sv_benchmark_vcf None
sv_benchmark_tbi None
sv_benchmark_bed None
fast5_dir None
bam demo_data/test.bam
ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
old_ref None
bed None
basecaller dorado
basecaller_chunk_size 25
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v4.0.0
basecaller_args None
basecaller_basemod_threads 2
cuda_device cuda:all
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
basecaller_model_path None
remora_model_path None
qscore_filter 10
remora_cfg None
dorado_ext fast5
clair3_model_path None
phase_vcf False
use_longphase True
use_longphase_intermediate True
sample_name SAMPLE
ctg_name EMPTY
include_all_ctgs False
ref_pct_full 0.1
var_pct_full 0.7
GVCF False
snp_min_af 0.08
indel_min_af 0.15
vcf_fn EMPTY
min_contig_size 0
min_mq 5
min_cov 2
tr_bed None
sv_types DEL,INS
min_sv_length 30
max_sv_length 100000
min_read_support auto
min_read_support_limit 2
cluster_merge_pos 150
sniffles_args None
bin_size 500
modbam2bed_args None
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,process_label,min_sv_length,max_sv_length,min_read_support,min_read_support_limit
wf {'name': 'wf-human-variation', 'template_version': '195cab5', 'example_cmd': ['--snp', '--sv', '--bam demo_data/demo.bam', '--bed demo_data/demo.bed', '--ref demo_data/demo.fasta', '--basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v4.0.0', '--sample_name MY_SAMPLE'], 'agent': 'cw-ci', 'e2l_base_tag': 'shaa6d218582d6056ea970b73e61f138ebb0ce6c5b1', 'e2l_snp_tag': 'sha800ab96e243576f7f5fb17a7c4ead9e538a48931', 'e2l_sv_tag': 'mr61_sha976a5388070d569f510d3fda2d4dc1a7aea97bae', 'e2l_methyl_tag': 'sha44a13bcf48db332b2277bb9f95b56d64e393a1d5', 'basecaller_container': 'dorado:sha097d9c8abc39b8266e3ee58f531f5ef8944a02c3', 'cnv_tag': 'shaa2eb8d075b9a8da6d5b8be6c29c2b7b772000f2b'}