Detailed view of 95-39687
Strain
| ID | 65 |
|---|---|
| Name | HXB22 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB22_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0532 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0532 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 37.6 |
| 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 | 95-39687 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 79 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39687.LR1 | 95-39687.SN1 | 95-39687.GH1 | 95-39687.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/HXB22 | supernova_results/HXB22 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-06 | 2020-01-22 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39687.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1551630 |
| mean_dna_per_gem | 750082.9409 |
| bc_on_whitelist | 0.9230120103 |
| bc_mean_qscore | 36.32923043 |
| n50_linked_reads_per_molecule | 17 |
| corrected_loaded_mass_ng | 1.76447664 |
| snps_phased | 0.8867176214 |
| genes_phased_lt_100kb | 0.852915952 |
| longest_phase_block | 1945530 |
| n50_phase_block | 98821 |
| molecule_length_mean | 34494.31698 |
| molecule_length_stddev | 46221.04342 |
| number_reads | 1099266760 |
| median_insert_size | 307 |
| mean_depth | 49.87898979 |
| zero_coverage | 0.02126320686 |
| mapped_reads | 0.9457210186 |
| pcr_duplication | 0.04880589663 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9518905096 |
| r1_q30_bases_fract | 0.9065959962 |
| r2_q20_bases_fract | 0.9404263304 |
| r2_q30_bases_fract | 0.8882475855 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863360515 |
| bc_q30_bases_fract | 0.9606763285 |
| large_sv_calls | 2360 |
| short_deletion_calls | 32658 |
Deepvariant results
| index | 749 | 750 | 751 | 752 | 753 | 754 | 755 | 756 | 757 | 758 | 759 | 760 | 761 | 762 | 763 | 764 | 765 | 766 | 767 | 768 | 769 | 770 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.DV1 | 95-39687.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 | 43491 | 33032 | 22879 | 35364 | 48904 | 33090 | 32417 | 47266 | 27445 | 26632 | 77414 | 17913 | 81873 | 62916 | 46030 | 77707 | 63786 | 49799 | 61596 | 44970 | 51548 | 408 |
| Biallelic_Insertion | 41614 | 30712 | 21194 | 33353 | 44748 | 31407 | 29939 | 42017 | 25886 | 24286 | 74117 | 17211 | 78218 | 58497 | 44311 | 70563 | 58763 | 47616 | 55822 | 41454 | 48269 | 600 |
| Biallelic_SNP | 143020 | 136042 | 44143 | 79098 | 213798 | 94901 | 101015 | 197083 | 72310 | 94438 | 255904 | 17238 | 311455 | 211860 | 96528 | 301275 | 277527 | 202039 | 256990 | 163165 | 133273 | 2768 |
| Multiallelic_Complex | 1122 | 682 | 536 | 716 | 1036 | 786 | 640 | 948 | 568 | 650 | 1981 | 354 | 1885 | 1467 | 997 | 1559 | 1368 | 1310 | 1441 | 1055 | 835 | 14 |
| Multiallelic_Deletion | 1913 | 1263 | 444 | 895 | 1835 | 866 | 902 | 1928 | 737 | 822 | 1941 | 191 | 2335 | 2278 | 1094 | 2982 | 2384 | 1630 | 2907 | 1504 | 1444 | 34 |
| Multiallelic_Insertion | 3718 | 2540 | 1087 | 1586 | 3492 | 1579 | 1725 | 3887 | 1454 | 1635 | 4026 | 519 | 4551 | 4289 | 2129 | 5518 | 4521 | 3287 | 5383 | 2863 | 2285 | 45 |
| Multiallelic_SNP | 71 | 48 | 52 | 42 | 127 | 86 | 81 | 117 | 43 | 186 | 302 | 16 | 256 | 118 | 48 | 111 | 309 | 202 | 125 | 172 | 92 | 1 |
| RefCall | 287160 | 210195 | 169773 | 244192 | 289808 | 261054 | 209750 | 261736 | 185816 | 192836 | 692787 | 135502 | 634976 | 415976 | 358555 | 436030 | 433742 | 378972 | 343123 | 310399 | 453413 | 28288 |
| Transition | 91408 | 84991 | 23862 | 44572 | 131827 | 55096 | 59841 | 127143 | 43308 | 56274 | 143295 | 7198 | 179104 | 130282 | 54151 | 186417 | 167343 | 118933 | 165215 | 98167 | 70736 | 1461 |
| Transversion | 51612 | 51051 | 20281 | 34526 | 81971 | 39805 | 41174 | 69940 | 29002 | 38164 | 112609 | 10040 | 132351 | 81578 | 42377 | 114858 | 110184 | 83106 | 91775 | 64998 | 62537 | 1307 |
Supernova results
| Analysis_ID | 95-39687.SN1 |
|---|---|
| assembly_size | 2459970824 |
| barcode_fraction | 1 |
| bases_per_read | 137.692 |
| bridge_1_50 | 43.278 |
| bridge_50 | 0.041 |
| bridge_model_badness_of_fit | 1.1228 |
| checksum | -2.24324e+18 |
| contig_N50 | 35906 |
| dinucleotide_percent | 1.1624 |
| dup_perc | 15.6256 |
| edge_N50 | 8578 |
| effective_coverage | 39.1036 |
| est_genome_size | 3060000000 |
| gc_percent | 42.0165 |
| hetdist | 35640 |
| high_AT_index | 0.074628 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 25291.8 |
| m10 | 2.63186 |
| median_ins_sz | 322 |
| nreads | 1099266760 |
| p10 | 58.5882 |
| phase_block_N50 | 30065 |
| placed_perc | 63.9594 |
| proper_pairs_perc | 92.7436 |
| q30_r2_perc | 88.8248 |
| raw_coverage | 53.532 |
| read_rate_DF_1_threaded | 28.2947 |
| read_rate_IO_10_threaded | 2999.94 |
| read_rate_IO_1_threaded | 2339.89 |
| repfrac | 9.89038 |
| rpb_N50 | 806 |
| scaffold_N50 | 4322032 |
| scaffolds_10kb_plus | 5521 |
| scaffolds_1kb_plus | 35355 |
| unbar_perc | 7.6988 |
| valid_bc_perc | 92.3012 |