Detailed view of 95-35734
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_X |
| Sequencing_date | 2019-07-26 |
| Sequencing_facility | USUHS |
| Sequencing_notes | |
| Raw_data_dir_name | 95-35734 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 73 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-35734.LR1 | 95-35734.GH1 | 95-35734.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_clif | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-06-10 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-35734.LR1 |
|---|---|
| instrument_ids | E00356 |
| gems_detected | 1663567 |
| mean_dna_per_gem | 678453.1757 |
| bc_on_whitelist | 0.9009207201 |
| bc_mean_qscore | 38.15390879 |
| n50_linked_reads_per_molecule | 15 |
| corrected_loaded_mass_ng | 1.595976545 |
| snps_phased | 0.917686843 |
| genes_phased_lt_100kb | 0.8325407609 |
| longest_phase_block | 616695 |
| n50_phase_block | 73572 |
| molecule_length_mean | 45486.07931 |
| molecule_length_stddev | 43831.93164 |
| number_reads | 843174396 |
| median_insert_size | 312 |
| mean_depth | 37.43379338 |
| zero_coverage | 0.03899497909 |
| mapped_reads | 0.9384325256 |
| pcr_duplication | 0.05082629844 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9388694239 |
| r1_q30_bases_fract | 0.8786966902 |
| r2_q20_bases_fract | 0.8728855892 |
| r2_q30_bases_fract | 0.7750261683 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9894219075 |
| bc_q30_bases_fract | 0.9728499438 |
| large_sv_calls | 1928 |
| short_deletion_calls | 19348 |
Deepvariant results
| index | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.DV1 | 95-35734.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 | 28289 | 19110 | 21467 | 30074 | 28472 | 28150 | 25010 | 25983 | 21590 | 19704 | 64968 | 18710 | 60310 | 43428 | 41667 | 46930 | 37787 | 35175 | 32485 | 31186 | 40462 | 21 |
| Biallelic_Insertion | 33011 | 21894 | 21477 | 31753 | 30525 | 29849 | 25563 | 26954 | 23416 | 20200 | 70845 | 19260 | 65801 | 47066 | 44958 | 49630 | 40858 | 39138 | 35549 | 33262 | 40450 | 26 |
| Biallelic_SNP | 25625 | 19762 | 30127 | 25836 | 39430 | 44269 | 30752 | 29169 | 18698 | 31924 | 111796 | 16871 | 94147 | 48672 | 40560 | 46577 | 45837 | 67665 | 35081 | 41484 | 46269 | 894 |
| Multiallelic_Complex | 973 | 525 | 525 | 717 | 754 | 766 | 629 | 647 | 550 | 550 | 1977 | 436 | 1698 | 1235 | 1152 | 1150 | 975 | 1152 | 914 | 839 | 762 | 2578 |
| Multiallelic_Deletion | 282 | 136 | 120 | 251 | 252 | 254 | 186 | 196 | 161 | 153 | 638 | 134 | 594 | 375 | 340 | 309 | 255 | 291 | 283 | 271 | 252 | 495 |
| Multiallelic_Insertion | 880 | 457 | 599 | 622 | 686 | 632 | 508 | 596 | 487 | 551 | 1773 | 470 | 1470 | 1094 | 1072 | 1064 | 937 | 1035 | 807 | 785 | 671 | 399 |
| Multiallelic_SNP | 17 | 19 | 38 | 12 | 48 | 52 | 29 | 47 | 26 | 77 | 165 | 18 | 174 | 37 | 24 | 32 | 69 | 119 | 33 | 78 | 26 | |
| RefCall | 269424 | 191786 | 171663 | 250418 | 253252 | 264951 | 206261 | 224283 | 187995 | 186763 | 685548 | 148206 | 602447 | 394704 | 379896 | 385266 | 331324 | 356158 | 297023 | 287327 | 335807 | |
| Transition | 11044 | 8830 | 14152 | 10604 | 18042 | 21301 | 14031 | 13005 | 7920 | 15450 | 53200 | 7089 | 44354 | 21827 | 17838 | 20542 | 20300 | 33993 | 15551 | 19174 | 20274 | |
| Transversion | 14581 | 10932 | 15975 | 15232 | 21388 | 22968 | 16721 | 16164 | 10778 | 16474 | 58596 | 9782 | 49793 | 26845 | 22722 | 26035 | 25537 | 33672 | 19530 | 22310 | 25995 |