Detailed view of 95-39692
Strain
| ID | 70 |
|---|---|
| Name | HXB29 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB29_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0537 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0537 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 33.2 |
| 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 | 95-39692 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 93 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39692.LR1 | 95-39692.SN1 | 95-39692.GH1 | 95-39692.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/HXB29 | supernova_results/HXB29 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-11 | 2020-01-31 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39692.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1755240 |
| mean_dna_per_gem | 757937.9023 |
| bc_on_whitelist | 0.9214394701 |
| bc_mean_qscore | 36.33621448 |
| n50_linked_reads_per_molecule | 16 |
| corrected_loaded_mass_ng | 1.782954458 |
| snps_phased | 0.8886231636 |
| genes_phased_lt_100kb | 0.8529536762 |
| longest_phase_block | 1284186 |
| n50_phase_block | 97779 |
| molecule_length_mean | 31276.59676 |
| molecule_length_stddev | 48747.93718 |
| number_reads | 1301243616 |
| median_insert_size | 298 |
| mean_depth | 59.27104819 |
| zero_coverage | 0.02264531213 |
| mapped_reads | 0.9482668924 |
| pcr_duplication | 0.04935868126 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9533051248 |
| r1_q30_bases_fract | 0.9086871223 |
| r2_q20_bases_fract | 0.9426288304 |
| r2_q30_bases_fract | 0.8915904035 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9864616938 |
| bc_q30_bases_fract | 0.961093788 |
| large_sv_calls | 2178 |
| short_deletion_calls | 30830 |
Deepvariant results
| index | 859 | 860 | 861 | 862 | 863 | 864 | 865 | 866 | 867 | 868 | 869 | 870 | 871 | 872 | 873 | 874 | 875 | 876 | 877 | 878 | 879 | 880 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.DV1 | 95-39692.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 | 41452 | 29918 | 34821 | 47741 | 26955 | 32889 | 27219 | 40065 | 23163 | 23263 | 89618 | 19063 | 83114 | 77526 | 68098 | 69829 | 43426 | 49425 | 36949 | 41852 | 44085 | 411 |
| Biallelic_Insertion | 39038 | 28299 | 30144 | 43490 | 25606 | 30344 | 24777 | 35631 | 21808 | 20809 | 82500 | 17674 | 76735 | 69911 | 61812 | 62669 | 40637 | 45912 | 34968 | 38298 | 42119 | 550 |
| Biallelic_SNP | 127235 | 116786 | 133024 | 192624 | 41391 | 93413 | 56221 | 146454 | 40704 | 63187 | 331825 | 26564 | 300074 | 336426 | 273087 | 241750 | 103730 | 193454 | 85241 | 142839 | 81836 | 2874 |
| Multiallelic_Complex | 1043 | 645 | 790 | 945 | 545 | 712 | 532 | 860 | 438 | 526 | 2144 | 358 | 1681 | 1611 | 1423 | 1317 | 897 | 1248 | 731 | 887 | 801 | 18 |
| Multiallelic_Deletion | 1768 | 916 | 1514 | 1775 | 378 | 788 | 530 | 1437 | 495 | 663 | 3044 | 255 | 2469 | 3224 | 2464 | 2405 | 1064 | 1777 | 929 | 1169 | 843 | 40 |
| Multiallelic_Insertion | 3370 | 1851 | 2934 | 3113 | 775 | 1487 | 1004 | 2787 | 898 | 1368 | 5756 | 626 | 4671 | 5998 | 4660 | 4454 | 2168 | 3480 | 1932 | 2327 | 1513 | 65 |
| Multiallelic_SNP | 80 | 49 | 138 | 76 | 46 | 93 | 57 | 135 | 27 | 99 | 308 | 18 | 236 | 180 | 93 | 97 | 134 | 187 | 56 | 161 | 59 | 2 |
| RefCall | 257165 | 185054 | 187628 | 252247 | 210758 | 239616 | 180726 | 233133 | 159401 | 177391 | 666879 | 128968 | 571295 | 431493 | 379676 | 379959 | 299471 | 352669 | 269134 | 283746 | 435137 | 28899 |
| Transition | 80086 | 70326 | 85223 | 110455 | 19058 | 54485 | 30954 | 91900 | 22592 | 37375 | 197363 | 13423 | 178044 | 210178 | 166649 | 148054 | 57954 | 118161 | 48420 | 84426 | 41136 | 1502 |
| Transversion | 47149 | 46460 | 47801 | 82169 | 22333 | 38928 | 25267 | 54554 | 18112 | 25812 | 134462 | 13141 | 122030 | 126248 | 106438 | 93696 | 45776 | 75293 | 36821 | 58413 | 40700 | 1372 |
Supernova results
| Analysis_ID | 95-39692.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 |