Detailed view of 95-39667
Strain
| ID | 53 |
|---|---|
| Name | BXH6 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH6_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0512 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0512 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 31.6 |
| 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 | 95-39667 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 89 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39667.LR1 | 95-39667.SN1 | 95-39667.GH1 | 95-39667.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/BXH6 | supernova_results/BXH6 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-09-26 | 2020-02-29 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39667.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1758030 |
| mean_dna_per_gem | 709279.7483 |
| bc_on_whitelist | 0.9263227995 |
| bc_mean_qscore | 36.44874512 |
| n50_linked_reads_per_molecule | 19 |
| corrected_loaded_mass_ng | 1.668492215 |
| snps_phased | 0.8985588838 |
| genes_phased_lt_100kb | 0.9009314141 |
| longest_phase_block | 1781027 |
| n50_phase_block | 178951 |
| molecule_length_mean | 40813.60587 |
| molecule_length_stddev | 52918.90686 |
| number_reads | 1264654212 |
| median_insert_size | 336 |
| mean_depth | 58.54794853 |
| zero_coverage | 0.02252970514 |
| mapped_reads | 0.9569529366 |
| pcr_duplication | 0.05245290959 |
| on_target_bases | |
| r1_q20_bases_fract | 0.962222779 |
| r1_q30_bases_fract | 0.9240149907 |
| r2_q20_bases_fract | 0.9528308651 |
| r2_q30_bases_fract | 0.9064484834 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9888913612 |
| bc_q30_bases_fract | 0.967773845 |
| large_sv_calls | 2336 |
| short_deletion_calls | 35418 |
Deepvariant results
| index | 507 | 508 | 509 | 510 | 511 | 512 | 513 | 514 | 515 | 516 | 517 | 518 | 519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | 527 | 528 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.DV1 | 95-39667.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 | 42725 | 24304 | 32444 | 29898 | 37826 | 27339 | 24669 | 25471 | 37406 | 26325 | 87047 | 28256 | 79648 | 66099 | 74959 | 69464 | 58704 | 50300 | 39136 | 40739 | 39800 | 98 |
| Biallelic_Insertion | 39356 | 22908 | 28197 | 27347 | 34417 | 25477 | 22276 | 23243 | 33347 | 23289 | 79505 | 24982 | 73545 | 59889 | 66766 | 61973 | 53517 | 46756 | 36073 | 36877 | 37862 | 222 |
| Biallelic_SNP | 131295 | 66548 | 117026 | 33653 | 124527 | 48716 | 37067 | 31716 | 144250 | 90330 | 324824 | 99842 | 289521 | 238300 | 307652 | 231157 | 238987 | 202262 | 91082 | 126078 | 53160 | 606 |
| Multiallelic_Complex | 1070 | 476 | 685 | 573 | 758 | 601 | 465 | 495 | 674 | 558 | 2051 | 546 | 1615 | 1357 | 1566 | 1380 | 1232 | 1248 | 859 | 874 | 686 | 9 |
| Multiallelic_Deletion | 1909 | 738 | 1241 | 535 | 1012 | 506 | 349 | 352 | 1489 | 775 | 2744 | 937 | 2255 | 2480 | 3107 | 2295 | 2023 | 1820 | 1198 | 1174 | 523 | 3 |
| Multiallelic_Insertion | 3751 | 1363 | 2404 | 928 | 1916 | 822 | 732 | 744 | 2723 | 1580 | 5126 | 1788 | 4296 | 4697 | 5935 | 4457 | 3997 | 3376 | 2399 | 2306 | 904 | 11 |
| Multiallelic_SNP | 72 | 51 | 135 | 20 | 82 | 61 | 38 | 52 | 54 | 189 | 358 | 109 | 211 | 112 | 108 | 104 | 327 | 222 | 58 | 159 | 46 | 26473 |
| RefCall | 240371 | 157701 | 170892 | 195256 | 211814 | 211088 | 163422 | 179644 | 170002 | 169695 | 616170 | 155239 | 519847 | 355832 | 349702 | 346291 | 365854 | 327866 | 245795 | 257457 | 377227 | 345 |
| Transition | 83480 | 40306 | 73706 | 15443 | 74178 | 24065 | 17869 | 14626 | 91829 | 53335 | 188568 | 62465 | 165891 | 147445 | 193671 | 139949 | 141295 | 121637 | 53945 | 74522 | 24282 | 261 |
| Transversion | 47815 | 26242 | 43320 | 18210 | 50349 | 24651 | 19198 | 17090 | 52421 | 36995 | 136256 | 37377 | 123630 | 90855 | 113981 | 91208 | 97692 | 80625 | 37137 | 51556 | 28878 |
Supernova results
| Analysis_ID | 95-39667.SN1 |
|---|---|
| assembly_size | 2533903167 |
| barcode_fraction | 1 |
| bases_per_read | 137.923 |
| bridge_1_50 | 12.153 |
| bridge_50 | 0.18 |
| bridge_model_badness_of_fit | 1.01997 |
| checksum | -8.58898e+18 |
| contig_N50 | 33098 |
| dinucleotide_percent | 1.06518 |
| dup_perc | 14.7996 |
| edge_N50 | 7710 |
| effective_coverage | 49.4269 |
| est_genome_size | 2860000000 |
| gc_percent | 42.3112 |
| hetdist | 41794 |
| high_AT_index | 0.0760056 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 39576.9 |
| m10 | 3.29355 |
| median_ins_sz | 350 |
| nreads | 1264654212 |
| p10 | 94.7059 |
| phase_block_N50 | 124715 |
| placed_perc | 61.3429 |
| proper_pairs_perc | 91.9389 |
| q30_r2_perc | 90.6448 |
| raw_coverage | 65.9919 |
| read_rate_DF_1_threaded | 14.4372 |
| read_rate_IO_10_threaded | 2223.04 |
| read_rate_IO_1_threaded | 3249.68 |
| repfrac | 8.19778 |
| rpb_N50 | 820 |
| scaffold_N50 | 15028807 |
| scaffolds_10kb_plus | 11878 |
| scaffolds_1kb_plus | 48831 |
| unbar_perc | 7.36772 |
| valid_bc_perc | 92.6323 |