Detailed view of 95-39665
Strain
| ID | 51 |
|---|---|
| Name | BXH3 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH3_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0510 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0510 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 35.6 |
| 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 | 95-39665 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 85 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39665.LR1 | 95-39665.SN1 | 95-39665.GH1 | 95-39665.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/BXH3 | supernova_results/BXH3 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-02 | 2020-02-25 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39665.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1724138 |
| mean_dna_per_gem | 790607.8966 |
| bc_on_whitelist | 0.9207164395 |
| bc_mean_qscore | 36.44654128 |
| n50_linked_reads_per_molecule | 12 |
| corrected_loaded_mass_ng | 1.859806548 |
| snps_phased | 0.9016910302 |
| genes_phased_lt_100kb | 0.8410975128 |
| longest_phase_block | 716259 |
| n50_phase_block | 84865 |
| molecule_length_mean | 27462.70794 |
| molecule_length_stddev | 50924.55671 |
| number_reads | 1215606910 |
| median_insert_size | 314 |
| mean_depth | 55.64009533 |
| zero_coverage | 0.02260057981 |
| mapped_reads | 0.9513416537 |
| pcr_duplication | 0.0476594174 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9587769547 |
| r1_q30_bases_fract | 0.9190837638 |
| r2_q20_bases_fract | 0.9483464197 |
| r2_q30_bases_fract | 0.9009508621 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9888356172 |
| bc_q30_bases_fract | 0.9676442244 |
| large_sv_calls | 2139 |
| short_deletion_calls | 33310 |
Deepvariant results
| index | 463 | 464 | 465 | 466 | 467 | 468 | 469 | 470 | 471 | 472 | 473 | 474 | 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 | 484 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.DV1 | 95-39665.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 | 37461 | 31628 | 29646 | 35710 | 52605 | 28748 | 31747 | 33239 | 36407 | 19033 | 97166 | 20156 | 87993 | 77030 | 57954 | 66233 | 66677 | 56341 | 35971 | 44875 | 45928 | 111 |
| Biallelic_Insertion | 35409 | 29638 | 26294 | 33092 | 47057 | 27026 | 28886 | 30065 | 32793 | 17678 | 88213 | 18606 | 81595 | 69187 | 53020 | 59381 | 60244 | 51878 | 34198 | 40850 | 43860 | 262 |
| Biallelic_SNP | 95188 | 129529 | 100941 | 80711 | 239513 | 59602 | 95251 | 90434 | 143062 | 33617 | 382811 | 35044 | 348252 | 322885 | 176219 | 197175 | 301924 | 245513 | 71234 | 165455 | 93297 | 727 |
| Multiallelic_Complex | 965 | 709 | 606 | 664 | 1026 | 621 | 609 | 639 | 712 | 436 | 2361 | 401 | 1837 | 1580 | 1277 | 1423 | 1400 | 1397 | 865 | 982 | 768 | 6 |
| Multiallelic_Deletion | 1581 | 1207 | 1044 | 980 | 1964 | 621 | 936 | 923 | 1329 | 276 | 3773 | 342 | 2767 | 3258 | 2155 | 2519 | 2616 | 2209 | 949 | 1442 | 1184 | 4 |
| Multiallelic_Insertion | 3100 | 2190 | 2016 | 1608 | 3925 | 1191 | 1738 | 2002 | 2656 | 646 | 7152 | 779 | 5371 | 6265 | 3935 | 4501 | 5060 | 4375 | 2034 | 2834 | 1910 | 8 |
| Multiallelic_SNP | 63 | 56 | 117 | 39 | 127 | 63 | 96 | 74 | 68 | 64 | 315 | 18 | 245 | 134 | 73 | 97 | 314 | 208 | 45 | 174 | 61 | 25429 |
| RefCall | 238873 | 176472 | 167750 | 211080 | 254344 | 220491 | 183785 | 200861 | 177660 | 159475 | 640901 | 125207 | 549280 | 393251 | 335170 | 352904 | 388702 | 347671 | 249617 | 274667 | 410763 | 445 |
| Transition | 58276 | 79096 | 62173 | 45703 | 148880 | 31837 | 57739 | 55988 | 91200 | 16224 | 234579 | 18989 | 208171 | 202963 | 108731 | 122187 | 183886 | 150346 | 40276 | 100265 | 48701 | 282 |
| Transversion | 36912 | 50433 | 38768 | 35008 | 90633 | 27765 | 37512 | 34446 | 51862 | 17393 | 148232 | 16055 | 140081 | 119922 | 67488 | 74988 | 118038 | 95167 | 30958 | 65190 | 44596 |
Supernova results
| Analysis_ID | 95-39665.SN1 |
|---|---|
| assembly_size | 2459516722 |
| barcode_fraction | 1 |
| bases_per_read | 137.796 |
| bridge_1_50 | 53.504 |
| bridge_50 | 0.037 |
| bridge_model_badness_of_fit | 1.00888 |
| checksum | -4.57372e+17 |
| contig_N50 | 34422 |
| dinucleotide_percent | 1.15084 |
| dup_perc | 14.9652 |
| edge_N50 | 7454 |
| effective_coverage | 45.6645 |
| est_genome_size | 2960000000 |
| gc_percent | 42.0456 |
| hetdist | 35352 |
| high_AT_index | 0.0759896 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 24548 |
| m10 | 2.46345 |
| median_ins_sz | 330 |
| nreads | 1215606910 |
| p10 | 41.7353 |
| phase_block_N50 | 28029 |
| placed_perc | 66.5931 |
| proper_pairs_perc | 92.012 |
| q30_r2_perc | 90.0951 |
| raw_coverage | 61.3982 |
| read_rate_DF_1_threaded | 16.0079 |
| read_rate_IO_10_threaded | 2275.15 |
| read_rate_IO_1_threaded | 3193.43 |
| repfrac | 8.99605 |
| rpb_N50 | 788 |
| scaffold_N50 | 6188161 |
| scaffolds_10kb_plus | 4489 |
| scaffolds_1kb_plus | 31871 |
| unbar_perc | 7.92836 |
| valid_bc_perc | 92.0716 |