Detailed view of 95-39672
Strain
| ID | 48 |
|---|---|
| Name | BXH12 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH12_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0517 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0517 |
|---|---|
| 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 | 95-39672 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 103 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39672.LR1 | 95-39672.SN1 | 95-39672.GH1 | 95-39672.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/BXH12 | supernova_results/BXH12 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-14 | 2020-02-19 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39672.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1425005 |
| mean_dna_per_gem | 892845.6539 |
| bc_on_whitelist | 0.9257815433 |
| bc_mean_qscore | 36.43994798 |
| n50_linked_reads_per_molecule | 24 |
| corrected_loaded_mass_ng | 2.100308131 |
| snps_phased | 0.9050743877 |
| genes_phased_lt_100kb | 0.9118451504 |
| longest_phase_block | 2617601 |
| n50_phase_block | 204442 |
| molecule_length_mean | 38719.19323 |
| molecule_length_stddev | 60877.13529 |
| number_reads | 1456697630 |
| median_insert_size | 348 |
| mean_depth | 66.5313395 |
| zero_coverage | 0.02205769279 |
| mapped_reads | 0.9485034955 |
| pcr_duplication | 0.07087749317 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9575858536 |
| r1_q30_bases_fract | 0.9172333118 |
| r2_q20_bases_fract | 0.9436231561 |
| r2_q30_bases_fract | 0.8929368171 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9887571573 |
| bc_q30_bases_fract | 0.9670680336 |
| large_sv_calls | 2272 |
| short_deletion_calls | 36387 |
Deepvariant results
| index | 397 | 398 | 399 | 400 | 401 | 402 | 403 | 404 | 405 | 406 | 407 | 408 | 409 | 410 | 411 | 412 | 413 | 414 | 415 | 416 | 417 | 418 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.DV1 | 95-39672.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 | 45151 | 25261 | 33829 | 30032 | 29343 | 30956 | 24067 | 34019 | 26133 | 20941 | 84906 | 23396 | 91730 | 55922 | 74209 | 75506 | 61011 | 46163 | 36681 | 39919 | 39481 | 76 |
| Biallelic_Insertion | 41179 | 24208 | 29316 | 27537 | 27181 | 28448 | 21861 | 30751 | 24126 | 19049 | 78147 | 20878 | 83233 | 51351 | 66415 | 67715 | 55228 | 42729 | 34492 | 35997 | 37490 | 245 |
| Biallelic_SNP | 143713 | 82294 | 126502 | 33810 | 54365 | 78753 | 32500 | 104800 | 56185 | 47564 | 300845 | 64573 | 365861 | 175102 | 314168 | 296808 | 256713 | 161521 | 86027 | 115291 | 52621 | 597 |
| Multiallelic_Complex | 1141 | 539 | 672 | 529 | 582 | 639 | 436 | 702 | 497 | 444 | 1976 | 456 | 1880 | 1127 | 1490 | 1402 | 1205 | 1053 | 810 | 863 | 676 | 7 |
| Multiallelic_Deletion | 2217 | 657 | 1366 | 605 | 590 | 700 | 349 | 949 | 764 | 425 | 2673 | 611 | 3120 | 1922 | 3038 | 2436 | 2142 | 1620 | 904 | 1191 | 564 | 3 |
| Multiallelic_Insertion | 4120 | 1220 | 2697 | 920 | 1087 | 1214 | 620 | 1896 | 1383 | 913 | 4945 | 1171 | 5857 | 3373 | 5615 | 4997 | 4212 | 3008 | 1733 | 2206 | 904 | 5 |
| Multiallelic_SNP | 85 | 39 | 148 | 28 | 51 | 82 | 42 | 101 | 36 | 76 | 302 | 93 | 266 | 146 | 107 | 112 | 316 | 142 | 53 | 132 | 35 | 25470 |
| RefCall | 240592 | 157614 | 174396 | 193561 | 196100 | 215851 | 161629 | 205747 | 148330 | 160992 | 604068 | 144797 | 542174 | 348223 | 354432 | 355931 | 368965 | 304677 | 241404 | 248803 | 372371 | 347 |
| Transition | 91944 | 47413 | 80487 | 15586 | 28241 | 44355 | 14760 | 62714 | 33249 | 25966 | 175336 | 38621 | 219558 | 104849 | 196006 | 179491 | 153489 | 98178 | 47911 | 68195 | 23993 | 250 |
| Transversion | 51769 | 34881 | 46015 | 18224 | 26124 | 34398 | 17740 | 42086 | 22936 | 21598 | 125509 | 25952 | 146303 | 70253 | 118162 | 117317 | 103224 | 63343 | 38116 | 47096 | 28628 |
Supernova results
| Analysis_ID | 95-39672.SN1 |
|---|---|
| assembly_size | 2576926647 |
| barcode_fraction | 1 |
| bases_per_read | 137.734 |
| bridge_1_50 | 12.302 |
| bridge_50 | 0.252 |
| bridge_model_badness_of_fit | 1.0586 |
| checksum | -2.83328e+18 |
| contig_N50 | 31655 |
| dinucleotide_percent | 1.16678 |
| dup_perc | 16.9557 |
| edge_N50 | 8007 |
| effective_coverage | 53.2985 |
| est_genome_size | 2950000000 |
| gc_percent | 42.5353 |
| hetdist | 26351 |
| high_AT_index | 0.0739356 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 41183.9 |
| m10 | 3.8199 |
| median_ins_sz | 364 |
| nreads | 1456697630 |
| p10 | 73.4118 |
| phase_block_N50 | 173444 |
| placed_perc | 50.2614 |
| proper_pairs_perc | 91.7978 |
| q30_r2_perc | 89.2937 |
| raw_coverage | 73.696 |
| read_rate_DF_1_threaded | 19.2999 |
| read_rate_IO_10_threaded | 2504.35 |
| read_rate_IO_1_threaded | 3114.74 |
| repfrac | 8.85337 |
| rpb_N50 | 1212 |
| scaffold_N50 | 12084581 |
| scaffolds_10kb_plus | 16515 |
| scaffolds_1kb_plus | 59189 |
| unbar_perc | 7.42185 |
| valid_bc_perc | 92.5782 |