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 |