Detailed view of 95-39680
Strain
| ID | 57 |
|---|---|
| Name | HXB10 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB10_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0525 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0525 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 33.2 |
| 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 | 95-39680 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 92 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39680.LR1 | 95-39680.SN1 | 95-39680.GH1 | 95-39680.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/HXB10 | supernova_results/HXB10 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-23 | 2020-01-21 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39680.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1557383 |
| mean_dna_per_gem | 600127.6411 |
| bc_on_whitelist | 0.9238931473 |
| bc_mean_qscore | 36.42732968 |
| n50_linked_reads_per_molecule | 21 |
| corrected_loaded_mass_ng | 1.411725486 |
| snps_phased | 0.8902143336 |
| genes_phased_lt_100kb | 0.8540596095 |
| longest_phase_block | 1325150 |
| n50_phase_block | 107070 |
| molecule_length_mean | 29111.0643 |
| molecule_length_stddev | 52074.89292 |
| number_reads | 1300771960 |
| median_insert_size | 301 |
| mean_depth | 58.1291738 |
| zero_coverage | 0.02060358092 |
| mapped_reads | 0.9377533353 |
| pcr_duplication | 0.060387217 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9514416131 |
| r1_q30_bases_fract | 0.9082129785 |
| r2_q20_bases_fract | 0.9361774856 |
| r2_q30_bases_fract | 0.8835921527 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9884648773 |
| bc_q30_bases_fract | 0.9663872845 |
| large_sv_calls | 2997 |
| short_deletion_calls | 33102 |
Deepvariant results
| index | 573 | 574 | 575 | 576 | 577 | 578 | 579 | 580 | 581 | 582 | 583 | 584 | 585 | 586 | 587 | 588 | 589 | 590 | 591 | 592 | 593 | 594 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.DV1 | 95-39680.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 | 29823 | 28077 | 23936 | 49066 | 40117 | 35819 | 37518 | 29469 | 36507 | 26388 | 95014 | 17872 | 113584 | 61620 | 53583 | 61568 | 43347 | 39191 | 53179 | 51677 | 51220 | 430 |
| Biallelic_Insertion | 29914 | 26585 | 21514 | 44863 | 37190 | 33776 | 34166 | 27143 | 33054 | 23691 | 87964 | 16900 | 103827 | 57208 | 50222 | 56413 | 40795 | 38488 | 48611 | 46875 | 49019 | 574 |
| Biallelic_SNP | 51956 | 95989 | 50677 | 206230 | 144115 | 126454 | 142059 | 62580 | 140771 | 86343 | 397928 | 17550 | 569824 | 210733 | 157807 | 173391 | 106218 | 115372 | 194201 | 213560 | 132816 | 2933 |
| Multiallelic_Complex | 787 | 616 | 531 | 1009 | 863 | 854 | 732 | 650 | 749 | 685 | 2378 | 356 | 2508 | 1391 | 1187 | 1272 | 929 | 1041 | 1271 | 1217 | 926 | 18 |
| Multiallelic_Deletion | 763 | 1139 | 584 | 2002 | 1421 | 935 | 1273 | 785 | 1438 | 975 | 3555 | 217 | 4648 | 2150 | 1638 | 2080 | 1101 | 932 | 2452 | 2123 | 1571 | 32 |
| Multiallelic_Insertion | 1733 | 2026 | 1290 | 3657 | 2566 | 1795 | 2390 | 1570 | 2730 | 1912 | 6644 | 588 | 8812 | 4231 | 3001 | 3884 | 2194 | 2080 | 4498 | 3914 | 2741 | 57 |
| Multiallelic_SNP | 50 | 47 | 55 | 88 | 103 | 101 | 84 | 77 | 57 | 97 | 406 | 14 | 382 | 105 | 68 | 87 | 113 | 142 | 98 | 180 | 91 | 1 |
| RefCall | 230534 | 177991 | 160446 | 255822 | 242092 | 248549 | 203293 | 197575 | 186264 | 180092 | 689660 | 125624 | 653726 | 376457 | 341576 | 363984 | 293121 | 322237 | 292819 | 297764 | 452209 | 28245 |
| Transition | 28824 | 60233 | 28525 | 119601 | 88119 | 72010 | 87881 | 36473 | 89321 | 52805 | 236026 | 7343 | 346954 | 127443 | 93272 | 104550 | 59626 | 64299 | 124763 | 132822 | 71494 | 1571 |
| Transversion | 23132 | 35756 | 22152 | 86629 | 55996 | 54444 | 54178 | 26107 | 51450 | 33538 | 161902 | 10207 | 222870 | 83290 | 64535 | 68841 | 46592 | 51073 | 69438 | 80738 | 61322 | 1362 |
Supernova results
| Analysis_ID | 95-39680.SN1 |
|---|---|
| assembly_size | 2465225608 |
| barcode_fraction | 1 |
| bases_per_read | 137.474 |
| bridge_1_50 | 50.887 |
| bridge_50 | 0.057 |
| bridge_model_badness_of_fit | 1.01757 |
| checksum | -2.98027e+18 |
| contig_N50 | 33530 |
| dinucleotide_percent | 1.34762 |
| dup_perc | 16.4209 |
| edge_N50 | 7334 |
| effective_coverage | 44.919 |
| est_genome_size | 3110000000 |
| gc_percent | 42.1318 |
| hetdist | 31633 |
| high_AT_index | 0.0729236 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 25041.4 |
| m10 | 2.95855 |
| median_ins_sz | 319 |
| nreads | 1300771960 |
| p10 | 32.8529 |
| phase_block_N50 | 39971 |
| placed_perc | 59.482 |
| proper_pairs_perc | 91.9541 |
| q30_r2_perc | 88.3592 |
| raw_coverage | 62.3532 |
| read_rate_DF_1_threaded | 31.0005 |
| read_rate_IO_10_threaded | 3056.8 |
| read_rate_IO_1_threaded | 2361.31 |
| repfrac | 10.0885 |
| rpb_N50 | 978 |
| scaffold_N50 | 2096621 |
| scaffolds_10kb_plus | 8215 |
| scaffolds_1kb_plus | 41620 |
| unbar_perc | 7.61069 |
| valid_bc_perc | 92.3893 |