Detailed view of 95-39694
Strain
| ID | 44 |
|---|---|
| Name | BN-Lx/Cub |
| Type | Inbred |
| Living | False |
| Source | MCW |
| Note | RI founder |
Animal
| Animal_name | BN-Lx/Cub_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0539 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0539 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 31.8 |
| 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 | 95-39694 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 83 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39694.LR1 | 95-39694.SN1 | 95-39694.GH1 | 95-39694.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/BN-Lx_Cub | supernova_results/BN-Lx_Cub | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-02 | 2019-11-01 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39694.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1733435 |
| mean_dna_per_gem | 718198.2849 |
| bc_on_whitelist | 0.9238571658 |
| bc_mean_qscore | 36.33733162 |
| n50_linked_reads_per_molecule | 17 |
| corrected_loaded_mass_ng | 1.689471961 |
| snps_phased | 0.8722735413 |
| genes_phased_lt_100kb | 0.856685633 |
| longest_phase_block | 1538870 |
| n50_phase_block | 72028 |
| molecule_length_mean | 39170.44091 |
| molecule_length_stddev | 45927.04133 |
| number_reads | 1135145452 |
| median_insert_size | 291 |
| mean_depth | 51.98131713 |
| zero_coverage | 0.01959208503 |
| mapped_reads | 0.9509276138 |
| pcr_duplication | 0.04887714367 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9551072171 |
| r1_q30_bases_fract | 0.9110989499 |
| r2_q20_bases_fract | 0.9439072687 |
| r2_q30_bases_fract | 0.8926210042 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9864804711 |
| bc_q30_bases_fract | 0.9611628824 |
| large_sv_calls | 2223 |
| short_deletion_calls | 19799 |
Deepvariant results
| index | 309 | 310 | 311 | 312 | 313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.DV1 | 95-39694.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 | 26649 | 18208 | 20552 | 29798 | 27395 | 27047 | 24275 | 24961 | 20461 | 18885 | 63285 | 18107 | 59991 | 42466 | 40046 | 45141 | 36529 | 33830 | 34482 | 30295 | 40246 | 406 |
| Biallelic_Insertion | 27944 | 18400 | 19282 | 28248 | 26409 | 25911 | 22545 | 23693 | 20289 | 17919 | 61852 | 17118 | 58538 | 41129 | 38872 | 43011 | 35423 | 33756 | 33216 | 28629 | 38967 | 565 |
| Biallelic_SNP | 26495 | 19753 | 30621 | 32445 | 41087 | 47040 | 31102 | 29607 | 19405 | 33142 | 118730 | 17458 | 112600 | 58626 | 44641 | 47946 | 48641 | 69783 | 59158 | 43387 | 55386 | 2761 |
| Multiallelic_Complex | 777 | 409 | 450 | 655 | 666 | 715 | 464 | 543 | 430 | 457 | 1741 | 360 | 1471 | 983 | 865 | 911 | 784 | 952 | 841 | 722 | 634 | 19 |
| Multiallelic_Deletion | 447 | 290 | 233 | 592 | 485 | 413 | 325 | 318 | 345 | 283 | 1114 | 212 | 1117 | 711 | 693 | 598 | 532 | 565 | 849 | 442 | 460 | 29 |
| Multiallelic_Insertion | 1106 | 568 | 653 | 956 | 840 | 824 | 649 | 719 | 579 | 617 | 2252 | 505 | 2073 | 1499 | 1296 | 1333 | 1157 | 1238 | 1805 | 975 | 809 | 59 |
| Multiallelic_SNP | 21 | 20 | 39 | 29 | 50 | 69 | 34 | 45 | 18 | 76 | 181 | 11 | 171 | 53 | 33 | 42 | 93 | 100 | 30 | 82 | 43 | 28708 |
| RefCall | 239709 | 169872 | 160565 | 227267 | 230776 | 246437 | 184907 | 203806 | 165630 | 173393 | 639371 | 133894 | 559455 | 358239 | 338964 | 350111 | 299231 | 330372 | 275968 | 262660 | 412529 | 1415 |
| Transition | 11362 | 8755 | 14299 | 14861 | 18841 | 22471 | 14095 | 13175 | 8120 | 15965 | 56920 | 7282 | 55984 | 27783 | 20147 | 20986 | 21391 | 34791 | 31865 | 19968 | 25386 | 1346 |
| Transversion | 15133 | 10998 | 16322 | 17584 | 22246 | 24569 | 17007 | 16432 | 11285 | 17177 | 61810 | 10176 | 56616 | 30843 | 24494 | 26960 | 27250 | 34992 | 27293 | 23419 | 30000 |
Supernova results
| Analysis_ID | 95-39694.SN1 |
|---|---|
| assembly_size | |
| barcode_fraction | |
| bases_per_read | |
| bridge_1_50 | |
| bridge_50 | |
| bridge_model_badness_of_fit | |
| checksum | |
| contig_N50 | |
| dinucleotide_percent | |
| dup_perc | |
| edge_N50 | |
| effective_coverage | |
| est_genome_size | |
| gc_percent | |
| hetdist | |
| high_AT_index | |
| likely_sequencers | |
| lw_mean_mol_len | |
| m10 | |
| median_ins_sz | |
| nreads | |
| p10 | |
| phase_block_N50 | |
| placed_perc | |
| proper_pairs_perc | |
| q30_r2_perc | |
| raw_coverage | |
| read_rate_DF_1_threaded | |
| read_rate_IO_10_threaded | |
| read_rate_IO_1_threaded | |
| repfrac | |
| rpb_N50 | |
| scaffold_N50 | |
| scaffolds_10kb_plus | |
| scaffolds_1kb_plus | |
| unbar_perc | |
| valid_bc_perc |