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 |