Detailed view of 95-39664

Strain

ID 50
Name BXH2
Type RI
Living False
Source
Note

Animal

Animal_name BXH2_Rat1
Sex M
Age adult
Generation
Euthanasia_date 2018-08-01
Source Pravenec
Note

Tissue

ID 4512-JFI-0509
Type spleen
Transfer_History Pravenec to Chen to HudsonAlpha
Note None

Sequencing

DNA_source 4512-JFI-0509
Platform 10X Chromium
DNA_extraction_method HMW
DNA_concentration 35.2
DNA_target_length
DNA_extraction_facility HudsonAlpha
Library_kit 150bp_PE
Library_facility HudsonAlpha
Sequencing_instrument HiSeq_X
Sequencing_date 2019-09-01
Sequencing_facility USUHS
Sequencing_notes
Raw_data_dir_name 95-39664
Raw_data_format fastq.gz
Raw_data_file_size_GB 102
Raw_data_available_from Chen
Note None

Analysis

Analysis_ID 95-39664.LR1 95-39664.SN1 95-39664.GH1 95-39664.DV1
Software_name LongRanger Supernova GROC-SVs DeepVariant
Software_version 2.2.2 2.1.1 Udit_PR3 0.9.0-gpu
Results_dir longranger_results/BXH2 supernova_results/BXH2 grocsvs_HXB /data/10_TB/deepvar
Analysis_date 2019-10-03 2020-02-24 2020-03-02 2019-12-04
Note combined analysis of BN samples and HXB

LongRanger results

Analysis_ID 95-39664.LR1
instrument_ids A00735
gems_detected 1757342
mean_dna_per_gem 728352.652
bc_on_whitelist 0.927400564
bc_mean_qscore 36.45436885
n50_linked_reads_per_molecule 22
corrected_loaded_mass_ng 1.713358844
snps_phased 0.9460341459
genes_phased_lt_100kb 0.9346506924
longest_phase_block 6632015
n50_phase_block 230156
molecule_length_mean 37963.20505
molecule_length_stddev 54976.25372
number_reads 1464916118
median_insert_size 305
mean_depth 67.83279392
zero_coverage 0.01969877215
mapped_reads 0.9582567867
pcr_duplication 0.05492842452
on_target_bases
r1_q20_bases_fract 0.963038618
r1_q30_bases_fract 0.9253988299
r2_q20_bases_fract 0.9555124613
r2_q30_bases_fract 0.9111102831
si_q20_bases_fract NaN
si_q30_bases_fract NaN
bc_q20_bases_fract 0.9889534899
bc_q30_bases_fract 0.9681979298
large_sv_calls 2448
short_deletion_calls 35502

Deepvariant results

index 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462
Analysis_ID 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1 95-39664.DV1
Chr chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr1 chr20 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX chrY
Biallelic_Deletion 43162 30030 25987 39136 32658 31298 24941 35191 26525 24022 87199 23379 107398 52808 68228 76254 58218 45703 43274 43485 44381 78
Biallelic_Insertion 39866 28117 22973 35717 30137 28598 22486 31666 24394 21430 80381 20754 97716 48916 61931 68396 53105 42403 39791 39027 42126 232
Biallelic_SNP 131046 115621 66459 119039 81829 81065 38628 114578 60085 69451 301044 65001 499376 150063 270922 305661 218237 157391 130199 151094 84924 634
Multiallelic_Complex 1175 760 544 967 885 792 505 713 531 614 2776 470 2676 1320 1943 1590 1382 1299 997 1030 855 12
Multiallelic_Deletion 2002 825 696 849 586 694 357 1009 817 506 2371 608 3608 1332 1926 2564 1859 1235 1280 1363 1031 6
Multiallelic_Insertion 3691 1541 1503 1459 1024 1161 651 2006 1459 1055 4186 1223 6467 2439 3421 5019 3566 2281 2494 2382 1690 9
Multiallelic_SNP 86 34 56 49 96 93 44 111 29 97 233 101 332 127 72 145 148 137 78 187 49 25777
RefCall 223056 156831 151219 201183 204729 221150 158779 201628 145700 159507 611746 138408 572312 331964 319881 344187 283870 289421 242337 252726 413187 378
Transition 83300 70912 39360 63557 46748 45386 19100 69498 35705 39753 177338 38798 304073 87554 166635 185278 131093 95725 78025 90074 42988 256
Transversion 47746 44709 27099 55482 35081 35679 19528 45080 24380 29698 123706 26203 195303 62509 104287 120383 87144 61666 52174 61020 41936

Supernova results

Analysis_ID 95-39664.SN1
assembly_size 2575321228
barcode_fraction 1
bases_per_read 137.956
bridge_1_50 13.019
bridge_50 0.217
bridge_model_badness_of_fit 1.02332
checksum 1.1987577745532987e+18
contig_N50 30577
dinucleotide_percent 1.07839
dup_perc 15.6219
edge_N50 8175
effective_coverage 56.5317
est_genome_size 2880000000
gc_percent 42.451
hetdist 3490
high_AT_index 0.0737757
likely_sequencers NovaSeq
lw_mean_mol_len 38797.1
m10 3.91161
median_ins_sz 318
nreads 1464916118
p10 85.8529
phase_block_N50 1077878
placed_perc 51.4969
proper_pairs_perc 92.0791
q30_r2_perc 91.111
raw_coverage 76.0794
read_rate_DF_1_threaded 25.1703
read_rate_IO_10_threaded 2627.09
read_rate_IO_1_threaded 2616.85
repfrac 8.55676
rpb_N50 948
scaffold_N50 11323885
scaffolds_10kb_plus 16711
scaffolds_1kb_plus 62548
unbar_perc 7.25994
valid_bc_perc 92.7401