Detailed view of 95-39682
Strain
| ID | 59 |
|---|---|
| Name | HXB15 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB15_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0527 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0527 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 38.2 |
| 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 | 95-39682 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 87 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39682.LR1 | 95-39682.SN1 | 95-39682.GH1 | 95-39682.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/HXB15 | supernova_results/HXB15 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-23 | 2020-01-27 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39682.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1933302 |
| mean_dna_per_gem | 543135.9032 |
| bc_on_whitelist | 0.9102832186 |
| bc_mean_qscore | 36.41073703 |
| n50_linked_reads_per_molecule | 14 |
| corrected_loaded_mass_ng | 1.277659525 |
| snps_phased | 0.8906171487 |
| genes_phased_lt_100kb | 0.8442671984 |
| longest_phase_block | 1945944 |
| n50_phase_block | 99692 |
| molecule_length_mean | 20459.5777 |
| molecule_length_stddev | 52910.42224 |
| number_reads | 1235984554 |
| median_insert_size | 307 |
| mean_depth | 53.68604302 |
| zero_coverage | 0.02036271516 |
| mapped_reads | 0.921392029 |
| pcr_duplication | 0.05783934678 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9426900443 |
| r1_q30_bases_fract | 0.8958497584 |
| r2_q20_bases_fract | 0.9228112743 |
| r2_q30_bases_fract | 0.865942185 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9881052649 |
| bc_q30_bases_fract | 0.9655190125 |
| large_sv_calls | 2561 |
| short_deletion_calls | 33075 |
Deepvariant results
| index | 617 | 618 | 619 | 620 | 621 | 622 | 623 | 624 | 625 | 626 | 627 | 628 | 629 | 630 | 631 | 632 | 633 | 634 | 635 | 636 | 637 | 638 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.DV1 | 95-39682.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 | 29975 | 28548 | 21923 | 49095 | 50496 | 28819 | 38198 | 35463 | 25448 | 20828 | 84336 | 29808 | 96774 | 66808 | 39403 | 85935 | 36006 | 55990 | 43413 | 43722 | 49710 | 418 |
| Biallelic_Insertion | 30829 | 27672 | 20598 | 45098 | 46366 | 28203 | 34865 | 32334 | 24698 | 19738 | 80345 | 26930 | 91402 | 62278 | 39450 | 77640 | 36060 | 52709 | 41388 | 40737 | 48306 | 591 |
| Biallelic_SNP | 50249 | 105708 | 40324 | 205808 | 229228 | 68165 | 148378 | 106998 | 62598 | 47234 | 307387 | 116556 | 443951 | 254544 | 46568 | 374922 | 51142 | 245552 | 126238 | 159443 | 124763 | 2835 |
| Multiallelic_Complex | 852 | 643 | 482 | 1052 | 1141 | 710 | 818 | 784 | 549 | 488 | 2153 | 665 | 2118 | 1498 | 985 | 1820 | 853 | 1494 | 1083 | 992 | 841 | 12 |
| Multiallelic_Deletion | 830 | 947 | 371 | 1947 | 2105 | 519 | 1388 | 1170 | 637 | 511 | 2814 | 1081 | 3489 | 2548 | 709 | 3830 | 570 | 2354 | 1578 | 1411 | 1430 | 29 |
| Multiallelic_Insertion | 1840 | 1827 | 1036 | 3542 | 3827 | 1026 | 2650 | 2463 | 1280 | 1023 | 5222 | 2092 | 6794 | 4893 | 1365 | 7013 | 1220 | 4497 | 3111 | 2748 | 2277 | 47 |
| Multiallelic_SNP | 38 | 46 | 60 | 72 | 138 | 76 | 99 | 92 | 41 | 75 | 302 | 89 | 314 | 119 | 33 | 165 | 96 | 210 | 85 | 161 | 93 | 28114 |
| RefCall | 243977 | 194342 | 163060 | 273235 | 288752 | 246185 | 219277 | 223000 | 177162 | 177784 | 696554 | 175682 | 660599 | 419407 | 335878 | 444804 | 298411 | 381345 | 294424 | 300310 | 438477 | 1494 |
| Transition | 27887 | 63926 | 21190 | 119701 | 141434 | 34938 | 92133 | 67143 | 36523 | 26100 | 177289 | 73662 | 263883 | 156627 | 21321 | 234224 | 23058 | 152234 | 76859 | 95065 | 66036 | 1341 |
| Transversion | 22362 | 41782 | 19134 | 86107 | 87794 | 33227 | 56245 | 39855 | 26075 | 21134 | 130098 | 42894 | 180068 | 97917 | 25247 | 140698 | 28084 | 93318 | 49379 | 64378 | 58727 |
Supernova results
| Analysis_ID | 95-39682.SN1 |
|---|---|
| assembly_size | 2451733799 |
| barcode_fraction | 1 |
| bases_per_read | 136.925 |
| bridge_1_50 | 62.397 |
| bridge_50 | 0.036 |
| bridge_model_badness_of_fit | 1.03695 |
| checksum | -8.46958e+18 |
| contig_N50 | 34682 |
| dinucleotide_percent | 1.50632 |
| dup_perc | 16.6113 |
| edge_N50 | 8193 |
| effective_coverage | 39.0801 |
| est_genome_size | 3320000000 |
| gc_percent | 42.022 |
| hetdist | 36788 |
| high_AT_index | 0.0725805 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 24064.3 |
| m10 | 2.70549 |
| median_ins_sz | 331 |
| nreads | 1235984554 |
| p10 | 24.0882 |
| phase_block_N50 | 21098 |
| placed_perc | 56.8614 |
| proper_pairs_perc | 91.7685 |
| q30_r2_perc | 86.5942 |
| raw_coverage | 55.3255 |
| read_rate_DF_1_threaded | 33.3065 |
| read_rate_IO_10_threaded | 2914.03 |
| read_rate_IO_1_threaded | 3173 |
| repfrac | 11.7331 |
| rpb_N50 | 922 |
| scaffold_N50 | 2502112 |
| scaffolds_10kb_plus | 6519 |
| scaffolds_1kb_plus | 35818 |
| unbar_perc | 8.97168 |
| valid_bc_perc | 91.0283 |