Detailed view of 95-39676
Strain
| ID | 71 |
|---|---|
| Name | HXB3 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB3_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0521 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0521 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 32.4 |
| 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 | 95-39676 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 87 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39676.LR1 | 95-39676.SN1 | 95-39676.GH1 | 95-39676.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/HXB3 | supernova_results/HXB3 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-08 | 2020-02-13 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39676.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1462738 |
| mean_dna_per_gem | 796836.173 |
| bc_on_whitelist | 0.9220850762 |
| bc_mean_qscore | 36.32465436 |
| n50_linked_reads_per_molecule | 13 |
| corrected_loaded_mass_ng | 1.874457792 |
| snps_phased | 0.8908488062 |
| genes_phased_lt_100kb | 0.8341759353 |
| longest_phase_block | 1361793 |
| n50_phase_block | 92086 |
| molecule_length_mean | 28584.85149 |
| molecule_length_stddev | 54205.48989 |
| number_reads | 1212262856 |
| median_insert_size | 321 |
| mean_depth | 54.39858478 |
| zero_coverage | 0.02057450178 |
| mapped_reads | 0.9387975672 |
| pcr_duplication | 0.06161718132 |
| on_target_bases | |
| r1_q20_bases_fract | 0.948119518 |
| r1_q30_bases_fract | 0.9012436936 |
| r2_q20_bases_fract | 0.9330977214 |
| r2_q30_bases_fract | 0.8773830325 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9862328691 |
| bc_q30_bases_fract | 0.9604030817 |
| large_sv_calls | 2065 |
| short_deletion_calls | 32949 |
Deepvariant results
| index | 925 | 926 | 927 | 928 | 929 | 930 | 931 | 932 | 933 | 934 | 935 | 936 | 937 | 938 | 939 | 940 | 941 | 942 | 943 | 944 | 945 | 946 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.DV1 | 95-39676.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 | 35459 | 30474 | 28009 | 49289 | 53738 | 34792 | 39089 | 29175 | 25756 | 26220 | 86870 | 27520 | 82943 | 73149 | 55779 | 87294 | 36396 | 50161 | 43801 | 45107 | 49695 | 411 |
| Biallelic_Insertion | 34614 | 28898 | 24960 | 44970 | 48548 | 32796 | 35232 | 26872 | 24460 | 23512 | 80887 | 24817 | 77357 | 67200 | 52432 | 77730 | 35522 | 47461 | 41087 | 41275 | 46822 | 558 |
| Biallelic_SNP | 83632 | 120035 | 79274 | 204450 | 251729 | 115987 | 151081 | 60821 | 62412 | 85562 | 316619 | 97562 | 292730 | 309169 | 175669 | 375218 | 51402 | 197038 | 127156 | 166837 | 123462 | 2883 |
| Multiallelic_Complex | 929 | 630 | 654 | 994 | 1030 | 757 | 808 | 625 | 513 | 612 | 2178 | 571 | 1869 | 1552 | 1172 | 1727 | 772 | 1238 | 994 | 1015 | 843 | 18 |
| Multiallelic_Deletion | 1328 | 1090 | 926 | 1752 | 2042 | 889 | 1358 | 710 | 619 | 801 | 2815 | 863 | 2500 | 2933 | 1748 | 3590 | 572 | 1740 | 1571 | 1451 | 1347 | 31 |
| Multiallelic_Insertion | 2513 | 2020 | 1911 | 3380 | 3928 | 1605 | 2569 | 1364 | 1219 | 1585 | 5308 | 1674 | 4863 | 5356 | 3166 | 6679 | 1155 | 3395 | 3032 | 2802 | 2215 | 51 |
| Multiallelic_SNP | 46 | 41 | 54 | 82 | 147 | 93 | 93 | 71 | 32 | 95 | 297 | 109 | 250 | 207 | 51 | 153 | 92 | 188 | 92 | 166 | 79 | 1 |
| RefCall | 261475 | 195778 | 177823 | 269769 | 294688 | 260165 | 219498 | 217644 | 175653 | 191543 | 700045 | 170095 | 607945 | 448278 | 372978 | 445232 | 295924 | 370764 | 297376 | 304155 | 438423 | 28370 |
| Transition | 50767 | 72944 | 48666 | 118783 | 156564 | 65653 | 94052 | 34928 | 36476 | 51585 | 184941 | 60684 | 171768 | 191255 | 103582 | 234494 | 23136 | 119103 | 77184 | 100199 | 65212 | 1515 |
| Transversion | 32865 | 47091 | 30608 | 85667 | 95165 | 50334 | 57029 | 25893 | 25936 | 33977 | 131678 | 36878 | 120962 | 117914 | 72087 | 140724 | 28266 | 77935 | 49972 | 66638 | 58250 | 1368 |
Supernova results
| Analysis_ID | 95-39676.SN1 |
|---|---|
| assembly_size | 2458528837 |
| barcode_fraction | 1 |
| bases_per_read | 137.542 |
| bridge_1_50 | 48.107 |
| bridge_50 | 0.042 |
| bridge_model_badness_of_fit | 1.04555 |
| checksum | 7.49211320435936e+18 |
| contig_N50 | 36541 |
| dinucleotide_percent | 1.20958 |
| dup_perc | 17.4661 |
| edge_N50 | 8341 |
| effective_coverage | 40.9316 |
| est_genome_size | 3130000000 |
| gc_percent | 42.0075 |
| hetdist | 33288 |
| high_AT_index | 0.074506 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 24793.5 |
| m10 | 2.4423 |
| median_ins_sz | 339 |
| nreads | 1212262856 |
| p10 | 29.7353 |
| phase_block_N50 | 36392 |
| placed_perc | 61.0997 |
| proper_pairs_perc | 92.5162 |
| q30_r2_perc | 87.7383 |
| raw_coverage | 57.7266 |
| read_rate_DF_1_threaded | 13.3082 |
| read_rate_IO_10_threaded | 2188.18 |
| read_rate_IO_1_threaded | 2087.92 |
| repfrac | 10.2811 |
| rpb_N50 | 928 |
| scaffold_N50 | 4576190 |
| scaffolds_10kb_plus | 4900 |
| scaffolds_1kb_plus | 33061 |
| unbar_perc | 7.79149 |
| valid_bc_perc | 92.2085 |