Detailed view of 95-39686
Strain
| ID | 64 |
|---|---|
| Name | HXB21 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB21_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0531 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0531 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 34.4 |
| 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 | 95-39686 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 82 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39686.LR1 | 95-39686.SN1 | 95-39686.GH1 | 95-39686.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/HXB21 | supernova_results/HXB21 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-08 | 2020-01-30 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39686.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1584227 |
| mean_dna_per_gem | 628008.8325 |
| bc_on_whitelist | 0.9218048706 |
| bc_mean_qscore | 36.33075562 |
| n50_linked_reads_per_molecule | 18 |
| corrected_loaded_mass_ng | 1.477312514 |
| snps_phased | 0.885803451 |
| genes_phased_lt_100kb | 0.8370526316 |
| longest_phase_block | 1413438 |
| n50_phase_block | 94076 |
| molecule_length_mean | 30093.8962 |
| molecule_length_stddev | 47805.17988 |
| number_reads | 1143645528 |
| median_insert_size | 306 |
| mean_depth | 51.35976629 |
| zero_coverage | 0.02167457985 |
| mapped_reads | 0.9401563699 |
| pcr_duplication | 0.05252756287 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9487434485 |
| r1_q30_bases_fract | 0.9022016148 |
| r2_q20_bases_fract | 0.9354313378 |
| r2_q30_bases_fract | 0.8815132864 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863690471 |
| bc_q30_bases_fract | 0.9607639608 |
| large_sv_calls | 2645 |
| short_deletion_calls | 32810 |
Deepvariant results
| index | 727 | 728 | 729 | 730 | 731 | 732 | 733 | 734 | 735 | 736 | 737 | 738 | 739 | 740 | 741 | 742 | 743 | 744 | 745 | 746 | 747 | 748 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.DV1 | 95-39686.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 | 37820 | 23295 | 26126 | 49278 | 31493 | 46494 | 30450 | 36622 | 37850 | 27477 | 111199 | 23526 | 106659 | 57576 | 60498 | 51927 | 57410 | 56180 | 35719 | 34069 | 52015 | 390 |
| Biallelic_Insertion | 36350 | 22870 | 23550 | 45091 | 29892 | 42730 | 28067 | 33451 | 34361 | 24739 | 101616 | 21437 | 98461 | 53955 | 55724 | 48774 | 53390 | 52352 | 34615 | 32191 | 49053 | 563 |
| Biallelic_SNP | 93615 | 59151 | 69496 | 203857 | 73477 | 210766 | 82088 | 118969 | 150324 | 98962 | 501580 | 66475 | 504902 | 172008 | 201534 | 95987 | 210535 | 237238 | 70210 | 76957 | 141382 | 2749 |
| Multiallelic_Complex | 978 | 522 | 555 | 1025 | 658 | 961 | 600 | 800 | 793 | 653 | 2666 | 496 | 2317 | 1250 | 1390 | 1064 | 1209 | 1362 | 914 | 809 | 854 | 16 |
| Multiallelic_Deletion | 1632 | 628 | 716 | 1861 | 651 | 1692 | 766 | 1089 | 1491 | 960 | 4838 | 632 | 4062 | 1924 | 2186 | 1305 | 2025 | 2217 | 912 | 752 | 1524 | 34 |
| Multiallelic_Insertion | 3060 | 1202 | 1542 | 3545 | 1310 | 2986 | 1448 | 2251 | 2735 | 1800 | 8764 | 1289 | 7721 | 3590 | 4161 | 2356 | 3939 | 4386 | 1837 | 1468 | 2525 | 46 |
| Multiallelic_SNP | 58 | 46 | 73 | 81 | 57 | 149 | 55 | 97 | 73 | 182 | 406 | 90 | 316 | 87 | 72 | 69 | 142 | 164 | 53 | 101 | 83 | 1 |
| RefCall | 260705 | 184180 | 171239 | 277950 | 239321 | 286068 | 203259 | 230493 | 206926 | 192581 | 762547 | 162263 | 691036 | 397295 | 389413 | 367921 | 349195 | 382492 | 280345 | 275831 | 458042 | 28867 |
| Transition | 57180 | 34308 | 41630 | 118320 | 40683 | 128721 | 48686 | 74276 | 96135 | 59721 | 308543 | 39639 | 305165 | 104424 | 124216 | 53966 | 126633 | 145961 | 39384 | 42065 | 75243 | 1440 |
| Transversion | 36435 | 24843 | 27866 | 85537 | 32794 | 82045 | 33402 | 44693 | 54189 | 39241 | 193037 | 26836 | 199737 | 67584 | 77318 | 42021 | 83902 | 91277 | 30826 | 34892 | 66139 | 1309 |
Supernova results
| Analysis_ID | 95-39686.SN1 |
|---|---|
| assembly_size | 2461584367 |
| barcode_fraction | 1 |
| bases_per_read | 137.591 |
| bridge_1_50 | 50.677 |
| bridge_50 | 0.043 |
| bridge_model_badness_of_fit | 1.0681 |
| checksum | 4.94425261432956e+18 |
| contig_N50 | 36407 |
| dinucleotide_percent | 1.23643 |
| dup_perc | 16.026 |
| edge_N50 | 8402 |
| effective_coverage | 39.8865 |
| est_genome_size | 3090000000 |
| gc_percent | 42.0412 |
| hetdist | 35523 |
| high_AT_index | 0.0741004 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 24548 |
| m10 | 2.67003 |
| median_ins_sz | 323 |
| nreads | 1143645528 |
| p10 | 41.5588 |
| phase_block_N50 | 36737 |
| placed_perc | 62.1532 |
| proper_pairs_perc | 92.6177 |
| q30_r2_perc | 88.1513 |
| raw_coverage | 55.1872 |
| read_rate_DF_1_threaded | 28.1523 |
| read_rate_IO_10_threaded | 2653.06 |
| read_rate_IO_1_threaded | 3617.47 |
| repfrac | 9.9409 |
| rpb_N50 | 828 |
| scaffold_N50 | 2923178 |
| scaffolds_10kb_plus | 6385 |
| scaffolds_1kb_plus | 35640 |
| unbar_perc | 7.81951 |
| valid_bc_perc | 92.1805 |