Detailed view of 95-39666
Strain
| ID | 52 |
|---|---|
| Name | BXH5 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | BXH5_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0511 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0511 |
|---|---|
| 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 | 95-39666 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 96 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39666.LR1 | 95-39666.SN1 | 95-39666.GH1 | 95-39666.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/BXH5 | supernova_results/BXH5 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-01 | 2020-02-26 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39666.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1740604 |
| mean_dna_per_gem | 737404.7429 |
| bc_on_whitelist | 0.9267168869 |
| bc_mean_qscore | 36.45652591 |
| n50_linked_reads_per_molecule | 18 |
| corrected_loaded_mass_ng | 1.73465276 |
| snps_phased | 0.9021676606 |
| genes_phased_lt_100kb | 0.8844844845 |
| longest_phase_block | 2375459 |
| n50_phase_block | 171609 |
| molecule_length_mean | 34415.68148 |
| molecule_length_stddev | 55245.85974 |
| number_reads | 1363054922 |
| median_insert_size | 312 |
| mean_depth | 62.57018927 |
| zero_coverage | 0.02040950729 |
| mapped_reads | 0.953118501 |
| pcr_duplication | 0.05468253741 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9597886289 |
| r1_q30_bases_fract | 0.9207863298 |
| r2_q20_bases_fract | 0.9501283387 |
| r2_q30_bases_fract | 0.9034824609 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9890541787 |
| bc_q30_bases_fract | 0.9681783153 |
| large_sv_calls | 2371 |
| short_deletion_calls | 35404 |
Deepvariant results
| index | 485 | 486 | 487 | 488 | 489 | 490 | 491 | 492 | 493 | 494 | 495 | 496 | 497 | 498 | 499 | 500 | 501 | 502 | 503 | 504 | 505 | 506 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.DV1 | 95-39666.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 | 26622 | 18227 | 34016 | 46836 | 40637 | 46376 | 35882 | 30310 | 29464 | 20337 | 82463 | 26315 | 83444 | 77470 | 75445 | 65062 | 50875 | 51049 | 44165 | 37067 | 45417 | 88 |
| Biallelic_Insertion | 27109 | 18100 | 29583 | 42199 | 36895 | 42190 | 32185 | 27759 | 27023 | 18649 | 76493 | 23200 | 77134 | 69990 | 67857 | 58686 | 46921 | 46766 | 40924 | 33965 | 43204 | 243 |
| Biallelic_SNP | 29207 | 21118 | 128141 | 185244 | 144689 | 212568 | 129702 | 73495 | 87670 | 43618 | 279263 | 87124 | 302613 | 339787 | 324957 | 211100 | 185316 | 208423 | 140711 | 98319 | 91022 | 727 |
| Multiallelic_Complex | 702 | 381 | 730 | 886 | 816 | 940 | 688 | 628 | 565 | 468 | 1977 | 485 | 1914 | 1627 | 1585 | 1312 | 1092 | 1279 | 944 | 821 | 791 | 10 |
| Multiallelic_Deletion | 453 | 295 | 1435 | 1716 | 1329 | 1668 | 1148 | 707 | 923 | 406 | 2562 | 817 | 2710 | 3323 | 3229 | 2084 | 1537 | 2011 | 1488 | 952 | 1121 | 5 |
| Multiallelic_Insertion | 1088 | 586 | 2772 | 3209 | 2585 | 2981 | 2125 | 1443 | 1806 | 875 | 4848 | 1658 | 4924 | 6106 | 5933 | 3975 | 2902 | 3750 | 2963 | 1800 | 1915 | 13 |
| Multiallelic_SNP | 37 | 27 | 136 | 73 | 84 | 143 | 85 | 77 | 46 | 75 | 279 | 110 | 246 | 186 | 109 | 92 | 292 | 231 | 66 | 124 | 57 | 1 |
| RefCall | 207647 | 144911 | 175199 | 227178 | 229784 | 248921 | 187253 | 195866 | 158429 | 160682 | 609577 | 149319 | 537459 | 391970 | 356642 | 337934 | 351426 | 331542 | 257332 | 245376 | 413481 | 27001 |
| Transition | 12782 | 9407 | 81488 | 106228 | 87497 | 129538 | 78901 | 42842 | 54477 | 23326 | 162567 | 53844 | 179888 | 211332 | 203077 | 127440 | 107865 | 126892 | 84180 | 56250 | 46007 | 443 |
| Transversion | 16425 | 11711 | 46653 | 79016 | 57192 | 83030 | 50801 | 30653 | 33193 | 20292 | 116696 | 33280 | 122725 | 128455 | 121880 | 83660 | 77451 | 81531 | 56531 | 42069 | 45015 | 284 |
Supernova results
| Analysis_ID | 95-39666.SN1 |
|---|---|
| assembly_size | 2535166706 |
| barcode_fraction | 1 |
| bases_per_read | 137.852 |
| bridge_1_50 | 17.236 |
| bridge_50 | 0.152 |
| bridge_model_badness_of_fit | 1.06871 |
| checksum | 8.048397759722333e+18 |
| contig_N50 | 32129 |
| dinucleotide_percent | 1.16933 |
| dup_perc | 15.721 |
| edge_N50 | 7282 |
| effective_coverage | 51.0132 |
| est_genome_size | 2950000000 |
| gc_percent | 42.3161 |
| hetdist | 30193 |
| high_AT_index | 0.0753694 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 35473.7 |
| m10 | 3.43572 |
| median_ins_sz | 327 |
| nreads | 1363054922 |
| p10 | 62.4118 |
| phase_block_N50 | 134724 |
| placed_perc | 58.7539 |
| proper_pairs_perc | 91.9838 |
| q30_r2_perc | 90.3482 |
| raw_coverage | 69.0963 |
| read_rate_DF_1_threaded | 19.5019 |
| read_rate_IO_10_threaded | 2996.59 |
| read_rate_IO_1_threaded | 3635.94 |
| repfrac | 8.85767 |
| rpb_N50 | 904 |
| scaffold_N50 | 12795431 |
| scaffolds_10kb_plus | 12317 |
| scaffolds_1kb_plus | 52276 |
| unbar_perc | 7.32831 |
| valid_bc_perc | 92.6717 |