Detailed view of 95-39670
Strain
| ID | 46 |
|---|---|
| Name | BXH10 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH10_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0515 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0515 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 35 |
| 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 | 95-39670 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 85 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39670.LR1 | 95-39670.SN1 | 95-39670.GH1 | 95-39670.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/BXH10 | supernova_results/BXH10 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-09-30 | 2020-01-24 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39670.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1798671 |
| mean_dna_per_gem | 636233.8509 |
| bc_on_whitelist | 0.92883215 |
| bc_mean_qscore | 36.3306964 |
| n50_linked_reads_per_molecule | 16 |
| corrected_loaded_mass_ng | 1.496660844 |
| snps_phased | 0.8909089194 |
| genes_phased_lt_100kb | 0.8760884126 |
| longest_phase_block | 1366620 |
| n50_phase_block | 140531 |
| molecule_length_mean | 33017.12574 |
| molecule_length_stddev | 56301.75202 |
| number_reads | 1185195254 |
| median_insert_size | 345 |
| mean_depth | 54.68006207 |
| zero_coverage | 0.02199802162 |
| mapped_reads | 0.9546547948 |
| pcr_duplication | 0.06274618303 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9572121174 |
| r1_q30_bases_fract | 0.9144262635 |
| r2_q20_bases_fract | 0.9474595933 |
| r2_q30_bases_fract | 0.8964131251 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863158924 |
| bc_q30_bases_fract | 0.9609625718 |
| large_sv_calls | 2281 |
| short_deletion_calls | 33490 |
Deepvariant results
| index | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 | 361 | 362 | 363 | 364 | 365 | 366 | 367 | 368 | 369 | 370 | 371 | 372 | 373 | 374 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.DV1 | 95-39670.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 | 32856 | 31566 | 32975 | 32052 | 43957 | 26793 | 30609 | 33493 | 20651 | 18949 | 74567 | 20890 | 103861 | 70127 | 42873 | 66559 | 60783 | 46847 | 53622 | 47684 | 48466 | 104 |
| Biallelic_Insertion | 31979 | 29317 | 28669 | 29462 | 39816 | 25215 | 27486 | 30183 | 19833 | 17601 | 69988 | 18867 | 94697 | 63046 | 40461 | 60512 | 55404 | 43635 | 48582 | 43166 | 45715 | 306 |
| Biallelic_SNP | 68874 | 125054 | 120105 | 48803 | 167144 | 44753 | 80774 | 88606 | 20071 | 33252 | 204356 | 36113 | 460217 | 259770 | 63279 | 219347 | 232287 | 166529 | 200937 | 178050 | 111667 | 611 |
| Multiallelic_Complex | 818 | 646 | 715 | 608 | 837 | 579 | 537 | 675 | 368 | 436 | 1759 | 400 | 2041 | 1464 | 883 | 1287 | 1180 | 1121 | 1131 | 1002 | 787 | 6 |
| Multiallelic_Deletion | 927 | 1152 | 1251 | 641 | 1528 | 403 | 737 | 904 | 304 | 225 | 1928 | 401 | 3754 | 2730 | 910 | 1999 | 2014 | 1576 | 2074 | 1591 | 1163 | 2 |
| Multiallelic_Insertion | 1935 | 2117 | 2452 | 1200 | 2788 | 769 | 1392 | 1877 | 610 | 629 | 3691 | 888 | 7098 | 5157 | 1603 | 3831 | 4038 | 3065 | 4012 | 3204 | 1992 | 2 |
| Multiallelic_SNP | 42 | 66 | 125 | 23 | 87 | 63 | 67 | 79 | 25 | 85 | 188 | 14 | 273 | 129 | 35 | 89 | 142 | 157 | 86 | 171 | 52 | 25482 |
| RefCall | 237983 | 184267 | 181203 | 212622 | 239675 | 219383 | 184873 | 204765 | 149494 | 163666 | 604768 | 129338 | 597008 | 386994 | 313153 | 364388 | 324759 | 333312 | 293042 | 288124 | 414820 | 344 |
| Transition | 40477 | 76867 | 76019 | 25347 | 101117 | 21419 | 47909 | 54981 | 8715 | 16070 | 114792 | 20518 | 282152 | 163532 | 33221 | 132569 | 140778 | 101066 | 126735 | 109376 | 57966 | 267 |
| Transversion | 28397 | 48187 | 44086 | 23456 | 66027 | 23334 | 32865 | 33625 | 11356 | 17182 | 89564 | 15595 | 178065 | 96238 | 30058 | 86778 | 91509 | 65463 | 74202 | 68674 | 53701 |
Supernova results
| Analysis_ID | 95-39670.SN1 |
|---|---|
| assembly_size | 2479544773 |
| barcode_fraction | 1 |
| bases_per_read | 137.903 |
| bridge_1_50 | 18.043 |
| bridge_50 | 0.114 |
| bridge_model_badness_of_fit | 1.08698 |
| checksum | 8.835708810223982e+18 |
| contig_N50 | 35603 |
| dinucleotide_percent | 0.988495 |
| dup_perc | 16.4206 |
| edge_N50 | 7912 |
| effective_coverage | 45.1192 |
| est_genome_size | 2860000000 |
| gc_percent | 42.1166 |
| hetdist | 45307 |
| high_AT_index | 0.0764699 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 36186.8 |
| m10 | 2.63166 |
| median_ins_sz | 358 |
| nreads | 1185195254 |
| p10 | 56.0882 |
| phase_block_N50 | 45425 |
| placed_perc | 65.3484 |
| proper_pairs_perc | 91.872 |
| q30_r2_perc | 89.6413 |
| raw_coverage | 61.8795 |
| read_rate_DF_1_threaded | 27.5005 |
| read_rate_IO_10_threaded | 2657.53 |
| read_rate_IO_1_threaded | 2387.93 |
| repfrac | 8.1997 |
| rpb_N50 | 792 |
| scaffold_N50 | 10689469 |
| scaffolds_10kb_plus | 5923 |
| scaffolds_1kb_plus | 35806 |
| unbar_perc | 7.11678 |
| valid_bc_perc | 92.8832 |