At a glance

Modified rate (tumor)

0.6303

Modified rate (normal)

0.5341

DML

3,348

DMR

140

DML: differentially modified loci. DMR: differentially modified regions.

Modified base stats

Modified base summary table computed by modkit (subsample of up to 10,000 reads).

type base mod threshold pass_count pass_frac all_count all_frac filename
normal C 5mC 0.7558594 34792 0.4525141 39089 0.45770591 SAMPLE.normal.mod_summary.tsv
normal C C 0.7558594 38359 0.49890748 39786 0.4658673 SAMPLE.normal.mod_summary.tsv
normal C 5hmC 0.7558594 3735 0.048578415 6527 0.07642678 SAMPLE.normal.mod_summary.tsv
tumor C C 0.7441406 58017 0.3949986 60253 0.36970702 SAMPLE.tumor.mod_summary.tsv
tumor C 5hmC 0.7441406 7857 0.05349301 13234 0.08120264 SAMPLE.tumor.mod_summary.tsv
tumor C 5mC 0.7441406 81005 0.55150837 89488 0.5490903 SAMPLE.tumor.mod_summary.tsv

Differentially modified loci

Differentially modified loci (DMLs) distribution in the different chromosomes computed by DSS. Values shown are the median -log10(P-value) in 1.00M windows.

No differentially modified loci to show.

Differentially modified regions

Differentially modified regions computed by DSS.

Differentially modified regions along the genome.

Top and bottom 100 differentially modified regions for size, areaStat and diff.Methy.

Chromosome Start End Length nCG Avg. methylation (T) Avg. methylation (N) Diff. methylation |Diff. methylation| areaStat
chr20 21506822 21513693 6872 393 0.8171 0.137 0.6801 0.6801 11757.7731
chr20 21101883 21105659 3777 167 0.7476 0.1164 0.6312 0.6312 3831.8889
chr20 17119835 17122746 2912 24 0.0497 0.6009 -0.5512 0.5512 -295.3192
chr20 21960360 21962509 2150 39 0.0226 0.6871 -0.6645 0.6645 -788.0021
chr20 21636398 21638507 2110 22 0.058 0.5948 -0.5368 0.5368 -204.0951
chr20 21394579 21396579 2001 109 0.8744 0.2504 0.624 0.624 2999.2724
chr20 21099182 21101109 1928 89 0.7139 0.0546 0.6593 0.6593 2689.6377
chr20 21516267 21518126 1860 79 0.5642 0.0995 0.4647 0.4647 1152.8878
chr20 21397770 21399614 1845 37 0.8019 0.234 0.5679 0.5679 477.2381
chr20 21391279 21393061 1783 74 0.8948 0.1951 0.6997 0.6997 2176.5977
chr20 22033572 22035255 1684 7 0.0117 0.6926 -0.6809 0.6809 -70.3363
chr20 17955460 17956829 1370 16 0.8388 0.1015 0.7373 0.7373 303.1441
chr20 18035880 18037097 1218 31 0.9047 0.4453 0.4594 0.4594 264.894
chr20 21019722 21020915 1194 54 0.8162 0.1589 0.6573 0.6573 1258.0475
chr20 18002915 18004068 1154 22 0.8713 0.2753 0.5961 0.5961 320.5726
chr20 21984336 21985481 1146 29 0.0195 0.6195 -0.6 0.6 -456.4418
chr20 21916228 21917316 1089 32 0.0149 0.5813 -0.5664 0.5664 -516.4055
chr20 21603619 21604633 1015 13 0.0519 0.5602 -0.5083 0.5083 -113.3117
chr20 17964630 17965640 1011 13 0.5638 0.01 0.5539 0.5539 148.0423
chr20 17310002 17310995 994 14 0.0641 0.5658 -0.5017 0.5017 -130.8505
chr20 15081995 15082978 984 6 0.774 0.1524 0.6216 0.6216 45.9108
chr20 15144732 15145680 949 7 0.8703 0.2328 0.6375 0.6375 63.879
chr20 21804572 21805517 946 18 0.0115 0.5497 -0.5382 0.5382 -189.8891
chr20 15033918 15034839 922 9 0.7585 0.0807 0.6778 0.6778 108.6836
chr20 17958760 17959663 904 10 0.772 0.1581 0.6139 0.6139 104.0617
chr20 21809560 21810434 875 40 0.1284 0.5617 -0.4332 0.4332 -381.8922
chr20 17943176 17944002 827 7 0.7277 0.1511 0.5766 0.5766 64.8983
chr20 17859228 17860017 790 23 0.8605 0.1487 0.7118 0.7118 569.5773
chr20 18030059 18030840 782 12 0.8403 0.3297 0.5106 0.5106 95.4401
chr20 22038081 22038856 776 11 0.0116 0.6974 -0.6859 0.6859 -94.8709
chr20 15077350 15078118 769 8 0.8433 0.262 0.5813 0.5813 69.2073
chr20 17615325 17616085 761 25 0.8463 0.3789 0.4673 0.4673 287.0004
chr20 17928499 17929251 753 24 0.8395 0.1298 0.7097 0.7097 522.2135
chr20 15008100 15008850 751 6 0.8726 0.2966 0.576 0.576 50.0132
chr20 17825767 17826486 720 9 0.7684 0.0496 0.7188 0.7188 135.5956
chr20 17538503 17539212 710 9 0.7587 0.0935 0.6652 0.6652 129.7452
chr20 17896322 17897030 709 8 0.7506 0.2165 0.534 0.534 79.5714
chr20 17518900 17519601 702 7 0.725 0.212 0.513 0.513 55.6147
chr20 18034734 18035409 676 10 0.9446 0.299 0.6456 0.6456 93.7172
chr20 21859199 21859869 671 11 0.0237 0.6071 -0.5834 0.5834 -123.5022
chr20 21106240 21106887 648 42 0.691 0.244 0.447 0.447 554.2312
chr20 18038797 18039441 645 7 0.7728 0.1777 0.5952 0.5952 47.3077
chr20 17882076 17882719 644 17 0.0184 0.693 -0.6747 0.6747 -301.709
chr20 17082856 17083494 639 18 0.0169 0.5733 -0.5564 0.5564 -248.0068
chr20 22009446 22010079 634 16 0.0116 0.6037 -0.5921 0.5921 -190.1301
chr20 17297057 17297682 626 9 0.0237 0.5001 -0.4765 0.4765 -68.7898
chr20 17903101 17903725 625 15 0.7932 0.2986 0.4946 0.4946 166.3244
chr20 21798292 21798902 611 8 0.0089 0.4813 -0.4724 0.4724 -72.5443
chr20 15061231 15061839 609 6 0.7491 0.1948 0.5543 0.5543 47.2528
chr20 21741744 21742351 608 7 0.0127 0.7184 -0.7057 0.7057 -75.3329
chr20 21545070 21545671 602 9 0.0616 0.5816 -0.52 0.52 -73.917
chr20 21641404 21641996 593 13 0.0134 0.5401 -0.5268 0.5268 -145.0908
chr20 15028915 15029506 592 6 0.8036 0.2337 0.5699 0.5699 51.6849
chr20 21671666 21672252 587 6 0.149 0.6776 -0.5286 0.5286 -45.2738
chr20 21722978 21723557 580 6 0.0057 0.5434 -0.5377 0.5377 -41.103
chr20 17900601 17901173 573 8 0.8291 0.1845 0.6446 0.6446 84.8015
chr20 15043587 15044157 571 6 0.705 0.1182 0.5868 0.5868 51.5162
chr20 17249227 17249785 559 18 0.0996 0.6383 -0.5388 0.5388 -208.6294
chr20 17960700 17961256 557 11 0.776 0.1666 0.6094 0.6094 149.246
chr20 21728822 21729375 554 20 0.144 0.5818 -0.4378 0.4378 -200.0546
chr20 17239533 17240086 554 10 0.0112 0.5047 -0.4936 0.4936 -95.1324
chr20 21652040 21652592 553 7 0.0106 0.6135 -0.6029 0.6029 -76.3925
chr20 21564376 21564926 551 17 0.0161 0.5589 -0.5429 0.5429 -214.2503
chr20 17773153 17773689 537 7 0.8572 0.266 0.5912 0.5912 75.0476
chr20 21888369 21888893 525 10 0.0196 0.479 -0.4594 0.4594 -96.9365
chr20 17319180 17319703 524 8 0.1183 0.704 -0.5857 0.5857 -85.6695
chr20 21895216 21895734 519 16 0.0089 0.4991 -0.4902 0.4902 -196.6868
chr20 17960009 17960507 499 12 0.8751 0.3908 0.4843 0.4843 108.8335
chr20 17549265 17549759 495 8 0.8762 0.4197 0.4565 0.4565 63.8494
chr20 22002840 22003333 494 14 0.0121 0.4869 -0.4748 0.4748 -140.0634
chr20 17450051 17450542 492 23 0.2948 0.7618 -0.4669 0.4669 -304.3374
chr20 15060098 15060585 488 9 0.8146 0.3417 0.4729 0.4729 73.8678
chr20 21862882 21863368 487 13 0.0687 0.5948 -0.5261 0.5261 -128.1222
chr20 15012738 15013219 482 8 0.8538 0.2589 0.595 0.595 84.4997
chr20 21441283 21441762 480 9 0.7949 0.2671 0.5278 0.5278 88.6973
chr20 17895662 17896140 479 17 0.6864 0.2142 0.4722 0.4722 170.4021
chr20 17649063 17649540 478 12 0.8245 0.2644 0.5601 0.5601 156.7811
chr20 21887675 21888146 472 26 0.0117 0.5101 -0.4984 0.4984 -399.4392
chr20 21646153 21646621 469 21 0.2667 0.7612 -0.4945 0.4945 -234.5979
chr20 21781442 21781899 458 22 0.0105 0.4541 -0.4437 0.4437 -278.3083
chr20 17064178 17064622 445 10 0.0617 0.6037 -0.542 0.542 -108.5035
chr20 17693737 17694165 429 17 0.1835 0.6777 -0.4941 0.4941 -204.7206
chr20 17347366 17347786 421 12 0.0221 0.543 -0.5208 0.5208 -137.9103
chr20 17843746 17844164 419 8 0.7402 0.1946 0.5456 0.5456 77.9033
chr20 21860983 21861399 417 6 0.0096 0.5552 -0.5456 0.5456 -51.4035
chr20 17208129 17208544 416 6 0.0244 0.5815 -0.557 0.557 -50.7602
chr20 17634918 17635330 413 11 0.8394 0.3445 0.4949 0.4949 119.5008
chr20 16944246 16944643 398 9 0.9731 0.1927 0.7804 0.7804 138.4411
chr20 21877446 21877840 395 14 0.015 0.5058 -0.4909 0.4909 -153.6327
chr20 22020802 22021192 391 6 0.0468 0.7454 -0.6986 0.6986 -60.1328
chr20 17166793 17167183 391 16 0.1842 0.7412 -0.557 0.557 -222.1121
chr20 17992371 17992759 389 10 0.846 0.2517 0.5943 0.5943 138.1842
chr20 21788703 21789090 388 8 0.0091 0.4485 -0.4393 0.4393 -68.5742
chr20 21786035 21786405 371 9 0.0078 0.483 -0.4752 0.4752 -85.9664
chr20 21547682 21548052 371 10 0.1593 0.7086 -0.5493 0.5493 -104.6588
chr20 17323020 17323387 368 6 0.0183 0.4531 -0.4348 0.4348 -53.1774
chr20 21728070 21728436 367 17 0.0195 0.5463 -0.5268 0.5268 -216.7764
chr20 21666225 21666589 365 9 0.048 0.5231 -0.4751 0.4751 -81.939
chr20 17279418 17279781 364 11 0.0815 0.5666 -0.4851 0.4851 -104.2597
chr20 22018008 22018366 359 13 0.0041 0.4656 -0.4615 0.4615 -134.0371
chr20 21473535 21473644 110 6 0.7005 0.2274 0.4731 0.4731 44.832
chr20 21800295 21800442 148 8 0.0028 0.5414 -0.5386 0.5386 -72.8335
chr20 17860451 17860608 158 6 0.8361 0.3873 0.4488 0.4488 47.3837
chr20 18032598 18032772 175 7 0.7337 0.2059 0.5277 0.5277 55.3453
chr20 21608524 21608707 184 13 0.041 0.4237 -0.3827 0.3827 -139.8579
chr20 15220955 15221145 191 6 0.0046 0.6023 -0.5976 0.5976 -57.5152
chr20 21647990 21648182 193 6 0.0059 0.5046 -0.4987 0.4987 -52.065
chr20 21744087 21744308 222 12 0.0137 0.4678 -0.4541 0.4541 -136.0824
chr20 21760973 21761197 225 8 0.048 0.594 -0.5461 0.5461 -79.1253
chr20 21831927 21832151 225 6 0.0106 0.4206 -0.4101 0.4101 -54.7596
chr20 17612571 17612795 225 8 0.8388 0.3505 0.4882 0.4882 77.1472
chr20 21452059 21452286 228 8 0.8109 0.2389 0.572 0.572 72.6078
chr20 21600680 21600920 241 7 0.0082 0.5851 -0.5769 0.5769 -102.9802
chr20 17878830 17879075 246 6 0.8609 0.0806 0.7803 0.7803 120.7259
chr20 21755242 21755492 251 11 0.0139 0.5053 -0.4914 0.4914 -108.5638
chr20 21264595 21264847 253 7 0.3413 0.8261 -0.4848 0.4848 -60.1032
chr20 21538286 21538538 253 19 0.1656 0.6625 -0.4969 0.4969 -234.2901
chr20 22028017 22028273 257 7 0.0057 0.6276 -0.6219 0.6219 -70.405
chr20 17683066 17683326 261 6 0.646 0.2042 0.4418 0.4418 53.3283
chr20 21856530 21856796 267 11 0.0215 0.4702 -0.4487 0.4487 -117.9789
chr20 21273774 21274045 272 8 0.3381 0.8053 -0.4671 0.4671 -72.799
chr20 17453693 17453964 272 22 0.1886 0.6291 -0.4405 0.4405 -209.0884
chr20 22046318 22046592 275 13 0.0188 0.6698 -0.651 0.651 -129.3751
chr20 17610669 17610945 277 10 0.8104 0.217 0.5933 0.5933 125.7664
chr20 15055855 15056132 278 10 0.8648 0.3978 0.467 0.467 94.4379
chr20 17330314 17330594 281 10 0.0315 0.5961 -0.5646 0.5646 -134.1958
chr20 18001618 18001914 297 6 0.0427 0.8226 -0.7798 0.7798 -111.7748
chr20 21679839 21680145 307 13 0.0093 0.4733 -0.464 0.464 -134.8371
chr20 20969854 20970170 317 9 0.669 0.1267 0.5422 0.5422 72.7095
chr20 17080338 17080660 323 8 0.0192 0.4857 -0.4665 0.4665 -68.0086
chr20 21090318 21090646 329 11 0.7383 0.309 0.4293 0.4293 100.7316
chr20 21915586 21915926 341 10 0.0046 0.4727 -0.4681 0.4681 -101.6851
chr20 21830763 21831104 342 10 0.0074 0.4713 -0.4639 0.4639 -109.1678
chr20 18029279 18029623 345 9 0.8576 0.3386 0.519 0.519 82.1695
chr20 18034134 18034482 349 6 0.7621 0.0298 0.7323 0.7323 87.5683
chr20 17973368 17973717 350 7 0.8257 0.2054 0.6203 0.6203 88.3742
chr20 21681574 21681923 350 12 0.0757 0.5083 -0.4325 0.4325 -127.8998
chr20 21557702 21558056 355 12 0.0664 0.5475 -0.4812 0.4812 -124.611
chr20 17710797 17711152 356 9 0.8221 0.3265 0.4956 0.4956 89.0545
chr20 21670509 21670866 358 21 0.1476 0.6612 -0.5136 0.5136 -289.1982

No differentially modified regions to show.

Software versions

Name Version
python 3.8.17
mod_kit 0.1.12
bgzip 1.18
R 4.3.1
DSS '2.48.0'
R 4.3.1
DSS '2.48.0'
R 4.3.1
DSS '2.48.0'
R 4.3.1
DSS '2.48.0'

Workflow parameters

Key Value
sv True
mod True
snv True
bam_normal wf-somatic-variation-demo/demo_normal.remap.bam
bam_tumor wf-somatic-variation-demo/demo_tumor.remap.bam
sample_name SAMPLE
ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna
bed None
tr_bed None
annotation True
out_dir output
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
annotation_threads 4
tumor_min_coverage 0
normal_min_coverage 0
depth_window_size 50000
depth_intervals False
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2
skip_haplotype_filter False
haplotype_filter_threads 4
ctg_name EMPTY
include_all_ctgs False
snv_min_af 0.05
indel_min_af 0.05
min_contig_size 0
min_qual 8
min_cov 4
use_longphase True
use_longphase_intermediate True
print_ref_calls False
print_germline_calls False
phase_normal False
clairs_debug False
fast_mode False
clair3_phase_vcf False
clair3_ref_pct_full 0.1
clair3_var_pct_full 0.7
clair3_min_mq 5
GVCF False
vcf_fn EMPTY
min_sv_length 20
nanomonsv_get_threads 4
classify_insert False
qv None
force_strand False
modkit_args None
dss_threads 1
modkit_threads 4
help False
version False
aws_image_prefix None
aws_queue None
disable_ping False
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
wf {'example_cmd': ['--snv', '--sv', '--mod', '--sample_name MYSAMPLE', '--ref wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna', '--bed wf-somatic-variation-demo/demo.bed', '--bam_normal wf-somatic-variation-demo/demo_normal.bam', '--bam_tumor wf-somatic-variation-demo/demo_tumor.bam', '--basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2'], 'container_sha': 'sha534c3242546d2cf9d8d56a2dd3e35643ac736919', 'container_snp_sha': 'sha426067c9633bbbbba10fa171a2935f809ce86636', 'container_sv_sha': 'shaa94980c361625f0d50dcaf5bcf2abd005d57ec2c', 'container_mod_sha': 'shac81dbea5f824cc43fd7aeb9ad99b4efe1503216e', 'common_sha': 'sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7', 'snpeff_tag': 'sha4f289afaf754c7a3e0b9ffb6c0b5be0f89a5cf04', 'dss_sha': 'sha75990241a7936bcb0dc9a72f2bd9623b40a02e4e', 'agent': None}