Detailed view of 95-39684
Strain
| ID | 61 |
|---|---|
| Name | HXB18 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB18_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0529 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0529 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 28.8 |
| 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 | 95-39684 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 101 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39684.LR1 | 95-39684.SN1 | 95-39684.GH1 | 95-39684.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/HXB18 | supernova_results/HXB18 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-01 | 2020-02-05 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39684.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1625024 |
| mean_dna_per_gem | 650751.5502 |
| bc_on_whitelist | 0.9275127388 |
| bc_mean_qscore | 36.3318706 |
| n50_linked_reads_per_molecule | 20 |
| corrected_loaded_mass_ng | 1.530811923 |
| snps_phased | 0.8955171883 |
| genes_phased_lt_100kb | 0.8578822515 |
| longest_phase_block | 1901466 |
| n50_phase_block | 91331 |
| molecule_length_mean | 28308.77419 |
| molecule_length_stddev | 51961.25574 |
| number_reads | 1424901594 |
| median_insert_size | 297 |
| mean_depth | 64.78938686 |
| zero_coverage | 0.02010329314 |
| mapped_reads | 0.9484159746 |
| pcr_duplication | 0.05794179374 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9537225381 |
| r1_q30_bases_fract | 0.9093256189 |
| r2_q20_bases_fract | 0.9435158331 |
| r2_q30_bases_fract | 0.8922299029 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863422837 |
| bc_q30_bases_fract | 0.9609621746 |
| large_sv_calls | 2621 |
| short_deletion_calls | 31790 |
Deepvariant results
| index | 661 | 662 | 663 | 664 | 665 | 666 | 667 | 668 | 669 | 670 | 671 | 672 | 673 | 674 | 675 | 676 | 677 | 678 | 679 | 680 | 681 | 682 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.DV1 | 95-39684.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 | 37739 | 20239 | 20558 | 45498 | 30064 | 38280 | 35282 | 30982 | 30941 | 18934 | 79978 | 25665 | 74726 | 76560 | 69971 | 76472 | 37837 | 54556 | 61382 | 43325 | 44213 | 389 |
| Biallelic_Insertion | 35873 | 19595 | 18894 | 41407 | 28203 | 35181 | 31905 | 27818 | 28152 | 17482 | 74727 | 23399 | 69691 | 69058 | 63288 | 68540 | 35893 | 50331 | 54927 | 39235 | 42667 | 557 |
| Biallelic_SNP | 107119 | 35040 | 31845 | 180306 | 65893 | 146457 | 127184 | 75194 | 100554 | 33709 | 266013 | 81260 | 238327 | 331482 | 286102 | 301092 | 65704 | 242368 | 257414 | 149170 | 84421 | 2923 |
| Multiallelic_Complex | 980 | 404 | 389 | 860 | 610 | 827 | 687 | 643 | 568 | 455 | 1914 | 478 | 1631 | 1639 | 1490 | 1582 | 736 | 1343 | 1460 | 938 | 800 | 13 |
| Multiallelic_Deletion | 1350 | 487 | 235 | 1549 | 636 | 1027 | 1125 | 804 | 1031 | 271 | 2383 | 695 | 2007 | 3348 | 2818 | 2745 | 655 | 2099 | 2927 | 1376 | 973 | 47 |
| Multiallelic_Insertion | 2707 | 872 | 683 | 2766 | 1164 | 1961 | 2021 | 1726 | 1919 | 627 | 4394 | 1447 | 3696 | 5969 | 5043 | 5280 | 1297 | 3853 | 5313 | 2543 | 1631 | 58 |
| Multiallelic_SNP | 45 | 31 | 55 | 78 | 67 | 103 | 97 | 81 | 50 | 80 | 308 | 27 | 245 | 187 | 99 | 137 | 119 | 249 | 136 | 133 | 88 | 3 |
| RefCall | 239626 | 157720 | 152292 | 240646 | 216245 | 250592 | 195353 | 206683 | 170287 | 163911 | 636281 | 138242 | 543440 | 409227 | 370033 | 383009 | 277382 | 353787 | 304454 | 270392 | 450196 | 29372 |
| Transition | 66548 | 19228 | 14975 | 101496 | 34847 | 84884 | 77508 | 44914 | 61559 | 16323 | 151449 | 49762 | 137124 | 208292 | 176360 | 184952 | 32298 | 145461 | 166241 | 89928 | 42795 | 1555 |
| Transversion | 40571 | 15812 | 16870 | 78810 | 31046 | 61573 | 49676 | 30280 | 38995 | 17386 | 114564 | 31498 | 101203 | 123190 | 109742 | 116140 | 33406 | 96907 | 91173 | 59242 | 41626 | 1368 |
Supernova results
| Analysis_ID | 95-39684.SN1 |
|---|---|
| assembly_size | 2474607613 |
| barcode_fraction | 1 |
| bases_per_read | 137.716 |
| bridge_1_50 | 56.682 |
| bridge_50 | 0.057 |
| bridge_model_badness_of_fit | 1.03925 |
| checksum | -3.72887e+17 |
| contig_N50 | 33207 |
| dinucleotide_percent | 1.1106 |
| dup_perc | 16.4479 |
| edge_N50 | 6913 |
| effective_coverage | 51.8634 |
| est_genome_size | 2970000000 |
| gc_percent | 42.1756 |
| hetdist | 25063 |
| high_AT_index | 0.0747473 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 24064.3 |
| m10 | 3.1082 |
| median_ins_sz | 312 |
| nreads | 1424901594 |
| p10 | 38.8529 |
| phase_block_N50 | 94027 |
| placed_perc | 60.0511 |
| proper_pairs_perc | 92.229 |
| q30_r2_perc | 89.223 |
| raw_coverage | 71.4925 |
| read_rate_DF_1_threaded | 26.6708 |
| read_rate_IO_10_threaded | 2762.68 |
| read_rate_IO_1_threaded | 3650.6 |
| repfrac | 8.78021 |
| rpb_N50 | 1042 |
| scaffold_N50 | 3448759 |
| scaffolds_10kb_plus | 7885 |
| scaffolds_1kb_plus | 42293 |
| unbar_perc | 7.24873 |
| valid_bc_perc | 92.7513 |