Detailed view of 95-39669
Strain
| ID | 55 |
|---|---|
| Name | BXH9 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH9_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0514 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0514 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 44.8 |
| 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 | 95-39669 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 77 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39669.LR1 | 95-39669.SN1 | 95-39669.GH1 | 95-39669.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/BXH9 | supernova_results/BXH9 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-02 | 2020-01-31 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39669.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1729077 |
| mean_dna_per_gem | 668369.2467 |
| bc_on_whitelist | 0.9274851783 |
| bc_mean_qscore | 36.34410288 |
| n50_linked_reads_per_molecule | 19 |
| corrected_loaded_mass_ng | 1.572255358 |
| snps_phased | 0.8963522016 |
| genes_phased_lt_100kb | 0.8940591823 |
| longest_phase_block | 1524766 |
| n50_phase_block | 168175 |
| molecule_length_mean | 42860.88007 |
| molecule_length_stddev | 51648.59667 |
| number_reads | 1081443878 |
| median_insert_size | 324 |
| mean_depth | 50.28557091 |
| zero_coverage | 0.02025842852 |
| mapped_reads | 0.9592439951 |
| pcr_duplication | 0.04484696922 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9598968573 |
| r1_q30_bases_fract | 0.9181166517 |
| r2_q20_bases_fract | 0.9520810272 |
| r2_q30_bases_fract | 0.9035365439 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9866486562 |
| bc_q30_bases_fract | 0.9616267973 |
| large_sv_calls | 2412 |
| short_deletion_calls | 33590 |
Deepvariant results
| index | 551 | 552 | 553 | 554 | 555 | 556 | 557 | 558 | 559 | 560 | 561 | 562 | 563 | 564 | 565 | 566 | 567 | 568 | 569 | 570 | 571 | 572 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.DV1 | 95-39669.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 | 31707 | 24354 | 21290 | 35111 | 31338 | 35180 | 31237 | 36950 | 37055 | 31071 | 86489 | 24025 | 96073 | 55133 | 58793 | 52617 | 46640 | 64176 | 42460 | 52951 | 40011 | 103 |
| Biallelic_Insertion | 30989 | 23212 | 19677 | 32355 | 29264 | 32457 | 28175 | 33248 | 33435 | 27450 | 79696 | 21804 | 87795 | 51167 | 53680 | 48542 | 43452 | 58163 | 39341 | 47646 | 38188 | 269 |
| Biallelic_SNP | 55365 | 65581 | 34016 | 73416 | 72024 | 112358 | 84416 | 116015 | 141811 | 120295 | 297721 | 63098 | 397646 | 153393 | 182470 | 106589 | 142820 | 299206 | 119935 | 207591 | 53879 | 643 |
| Multiallelic_Complex | 814 | 477 | 447 | 630 | 666 | 750 | 618 | 777 | 709 | 695 | 2093 | 464 | 2051 | 1153 | 1204 | 1011 | 950 | 1541 | 969 | 1117 | 644 | 8 |
| Multiallelic_Deletion | 861 | 765 | 266 | 820 | 599 | 884 | 764 | 1128 | 1419 | 1134 | 2716 | 604 | 3204 | 1451 | 1968 | 1217 | 1264 | 2691 | 1323 | 1996 | 470 | 1 |
| Multiallelic_Insertion | 1840 | 1365 | 761 | 1536 | 1162 | 1688 | 1390 | 2246 | 2494 | 2280 | 5201 | 1169 | 6118 | 2934 | 3722 | 2156 | 2403 | 5232 | 2665 | 3709 | 783 | 4 |
| Multiallelic_SNP | 46 | 36 | 43 | 31 | 65 | 96 | 38 | 72 | 58 | 183 | 299 | 20 | 267 | 76 | 61 | 51 | 256 | 271 | 62 | 122 | 49 | 1 |
| RefCall | 239449 | 174282 | 156291 | 225103 | 226618 | 248902 | 189797 | 218404 | 191065 | 190903 | 669786 | 140501 | 613574 | 369151 | 352529 | 345362 | 367110 | 382015 | 275944 | 295254 | 388615 | 25936 |
| Transition | 30812 | 39730 | 16717 | 41696 | 40016 | 65225 | 50196 | 72645 | 90133 | 74121 | 175059 | 38050 | 239542 | 89577 | 111886 | 59968 | 80610 | 186076 | 70845 | 129791 | 24793 | 383 |
| Transversion | 24553 | 25851 | 17299 | 31720 | 32008 | 47133 | 34220 | 43370 | 51678 | 46174 | 122662 | 25048 | 158104 | 63816 | 70584 | 46621 | 62210 | 113130 | 49090 | 77800 | 29086 | 260 |
Supernova results
| Analysis_ID | 95-39669.SN1 |
|---|---|
| assembly_size | 2480232820 |
| barcode_fraction | 1 |
| bases_per_read | 138.056 |
| bridge_1_50 | 9.723 |
| bridge_50 | 0.168 |
| bridge_model_badness_of_fit | 1.01161 |
| checksum | -1.96757e+18 |
| contig_N50 | 35947 |
| dinucleotide_percent | 0.975576 |
| dup_perc | 14.7956 |
| edge_N50 | 8400 |
| effective_coverage | 42.1667 |
| est_genome_size | 2870000000 |
| gc_percent | 42.089 |
| hetdist | 43424 |
| high_AT_index | 0.0770849 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 42856.1 |
| m10 | 2.66887 |
| median_ins_sz | 336 |
| nreads | 1081443878 |
| p10 | 102.647 |
| phase_block_N50 | 38739 |
| placed_perc | 67.6951 |
| proper_pairs_perc | 92.4394 |
| q30_r2_perc | 90.3537 |
| raw_coverage | 56.3367 |
| read_rate_DF_1_threaded | 27.0911 |
| read_rate_IO_10_threaded | 2983.13 |
| read_rate_IO_1_threaded | 3619.38 |
| repfrac | 8.27896 |
| rpb_N50 | 710 |
| scaffold_N50 | 15260788 |
| scaffolds_10kb_plus | 6039 |
| scaffolds_1kb_plus | 37571 |
| unbar_perc | 7.25148 |
| valid_bc_perc | 92.7485 |