Detailed view of 4512-JFI-0502

Strain

ID 4
Name BN/NHsdMcwi
Type Inbred
Living False
Source MCW
Note

Animal

Animal_name BN/NHsdMcwi_Eva
Sex F
Age adult
Generation
Euthanasia_date 2004-01-01
Source Dwinell
Note Eva, euthanized prior to 2004

Tissue

ID 4512-JFI-0495
Type lung
Transfer_History Dwinell to Chen to HudsonAlpha
Note None

Sequencing

DNA_source 4512-JFI-0495
Platform 10X Chromium
DNA_extraction_method HMW
DNA_concentration 46
DNA_target_length
DNA_extraction_facility HudsonAlpha
Library_kit 150bp_PE
Library_facility HudsonAlpha
Sequencing_instrument HiSeq_X10
Sequencing_date 2018-07-18
Sequencing_facility HudsonAlpha
Sequencing_notes Lanes per sample: 1
Raw_data_dir_name 4512-JFI-0502
Raw_data_format fastq.gz
Raw_data_file_size_GB 66
Raw_data_available_from Chen
Note None

Analysis

Analysis_ID 4512-JFI-0502.LR1 4512-JFI-0502.GH1 4512-JFI-0502.DV1
Software_name LongRanger GROC-SVs DeepVariant
Software_version 2.2.2 Udit_PR3 0.9.0-gpu
Results_dir longranger_results/0502_bn_eve grocsvs_HXB /data/10_TB/deepvar
Analysis_date 2018-07-29 2020-03-02 2019-12-04
Note combined analysis of BN samples and HXB

LongRanger results

Analysis_ID 4512-JFI-0502.LR1
instrument_ids E00431
gems_detected 1682085
mean_dna_per_gem 509217.5966
bc_on_whitelist 0.9090709552
bc_mean_qscore 38.34479891
n50_linked_reads_per_molecule 16
corrected_loaded_mass_ng 1.197870936
snps_phased 0.8674053511
genes_phased_lt_100kb 0.7097167225
longest_phase_block 714102
n50_phase_block 97035
molecule_length_mean 46742.82218
molecule_length_stddev 38385.8648
number_reads 791414428
median_insert_size 258
mean_depth 34.97643915
zero_coverage 0.04109502169
mapped_reads 0.9388256288
pcr_duplication 0.03494831763
on_target_bases
r1_q20_bases_fract 0.9585880476
r1_q30_bases_fract 0.9174511527
r2_q20_bases_fract 0.9045909055
r2_q30_bases_fract 0.8244299264
si_q20_bases_fract 0.9585842223
si_q30_bases_fract 0.9338895083
bc_q20_bases_fract 0.9913872475
bc_q30_bases_fract 0.9778665921
large_sv_calls 1699
short_deletion_calls 15181

Deepvariant results

index 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88
Analysis_ID 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.DV1 4512-JFI-0502.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 30850 21242 22136 32242 30761 29904 26555 27656 23440 20855 70035 19556 66162 47253 45183 50177 40635 38017 35165 33775 42256 29
Biallelic_Insertion 36686 24825 22322 35031 33926 33113 27950 29522 25994 22030 77943 20886 74285 52814 50881 55247 45249 43346 39543 36973 43744 19
Biallelic_SNP 29426 23439 31258 30076 42557 47613 33341 32500 22232 33942 119085 19134 102554 54486 46781 52615 50455 71948 39329 45794 51797 932
Multiallelic_Complex 1089 558 534 783 815 843 651 697 595 594 2125 485 1816 1312 1237 1278 1094 1171 989 883 793 1
Multiallelic_Deletion 284 152 158 235 257 253 190 192 190 180 631 138 566 396 353 378 302 315 286 248 247 2469
Multiallelic_Insertion 904 490 593 658 715 676 526 627 549 538 1811 417 1459 1120 1005 1051 913 1104 855 781 710 537
Multiallelic_SNP 21 31 40 26 46 80 41 67 30 66 187 21 187 45 36 46 75 110 40 113 56 395
RefCall 407976 291167 232509 376107 376817 382034 302545 325524 285610 260716 982180 210954 887677 597891 589478 586333 495123 513720 448699 420931 497045
Transition 13595 11154 15089 13328 20189 23448 15808 15223 10135 16827 58279 8577 49714 25738 21891 24429 23508 36850 18213 21969 23981
Transversion 15831 12285 16169 16748 22368 24165 17533 17277 12097 17115 60806 10557 52840 28748 24890 28186 26947 35098 21116 23825 27816

Supernova results