Detailed view of 95-39695
Strain
| ID | 45 |
|---|---|
| Name | SHR/OlaIpcv |
| Type | Inbred |
| Living | False |
| Source | MCW |
| Note | RI founder |
Animal
| Animal_name | SHR/OlaIpcv_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0540 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0540 |
|---|---|
| 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 | 95-39695 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 83 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39695.LR1 | 95-39695.SN1 | 95-39695.GH1 | 95-39695.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/SHR_OlaIpcv | supernova_results/SHR_OlaIpcv | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-16 | 2019-11-01 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39695.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1822362 |
| mean_dna_per_gem | 616900.2751 |
| bc_on_whitelist | 0.920320291 |
| bc_mean_qscore | 36.31782586 |
| n50_linked_reads_per_molecule | 13 |
| corrected_loaded_mass_ng | 1.451181017 |
| snps_phased | 0.9036557711 |
| genes_phased_lt_100kb | 0.8170332937 |
| longest_phase_block | 1040435 |
| n50_phase_block | 91999 |
| molecule_length_mean | 24420.2176 |
| molecule_length_stddev | 48040.86945 |
| number_reads | 1158437966 |
| median_insert_size | 296 |
| mean_depth | 51.81962318 |
| zero_coverage | 0.02559359176 |
| mapped_reads | 0.938078219 |
| pcr_duplication | 0.05216518442 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9482525375 |
| r1_q30_bases_fract | 0.9015543183 |
| r2_q20_bases_fract | 0.9349511736 |
| r2_q30_bases_fract | 0.8804347553 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9860051284 |
| bc_q30_bases_fract | 0.960183116 |
| large_sv_calls | 2311 |
| short_deletion_calls | 40568 |
Deepvariant results
| index | 1013 | 1014 | 1015 | 1016 | 1017 | 1018 | 1019 | 1020 | 1021 | 1022 | 1023 | 1024 | 1025 | 1026 | 1027 | 1028 | 1029 | 1030 | 1031 | 1032 | 1033 | 1034 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.DV1 | 95-39695.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 | 54133 | 36318 | 34646 | 49086 | 53816 | 45758 | 39872 | 47162 | 39779 | 33627 | 116289 | 30741 | 118370 | 83583 | 78343 | 86537 | 67897 | 63213 | 62712 | 55472 | 56154 | 128 |
| Biallelic_Insertion | 50033 | 33826 | 30384 | 45077 | 48484 | 42368 | 36142 | 41872 | 36044 | 29600 | 105963 | 27599 | 108175 | 76081 | 71191 | 77809 | 61874 | 57937 | 56584 | 50493 | 53402 | 327 |
| Biallelic_SNP | 210670 | 165884 | 132469 | 204796 | 253172 | 207109 | 162110 | 200110 | 166284 | 140322 | 548422 | 124662 | 603414 | 388880 | 347187 | 375842 | 310056 | 300790 | 267693 | 242712 | 162853 | 749 |
| Multiallelic_Complex | 1451 | 747 | 811 | 1043 | 1086 | 904 | 830 | 1015 | 818 | 793 | 2735 | 618 | 2505 | 1778 | 1651 | 1788 | 1456 | 1573 | 1377 | 1231 | 967 | 13 |
| Multiallelic_Deletion | 3086 | 1490 | 1540 | 1992 | 2169 | 1630 | 1498 | 1950 | 1634 | 1524 | 5120 | 1085 | 4655 | 3721 | 3394 | 3730 | 2744 | 2843 | 3025 | 2305 | 1829 | 3 |
| Multiallelic_Insertion | 5511 | 2680 | 2836 | 3439 | 4130 | 2961 | 2715 | 3691 | 3109 | 2669 | 9358 | 2109 | 8816 | 6746 | 6195 | 6692 | 5258 | 5229 | 5505 | 4244 | 3106 | 12 |
| Multiallelic_SNP | 105 | 81 | 141 | 80 | 149 | 143 | 113 | 142 | 67 | 189 | 445 | 102 | 369 | 227 | 134 | 161 | 325 | 273 | 151 | 183 | 96 | 1 |
| RefCall | 303882 | 217057 | 196133 | 277061 | 291928 | 280886 | 225367 | 266636 | 212975 | 208798 | 769499 | 182435 | 715506 | 473438 | 437379 | 453773 | 438386 | 404040 | 343269 | 331173 | 496112 | 26657 |
| Transition | 137713 | 103536 | 84870 | 119159 | 158173 | 126985 | 101394 | 128816 | 106686 | 88698 | 340540 | 78708 | 370229 | 244639 | 217906 | 234942 | 189671 | 187265 | 172867 | 151855 | 89183 | 453 |
| Transversion | 72957 | 62348 | 47599 | 85637 | 94999 | 80124 | 60716 | 71294 | 59598 | 51624 | 207882 | 45954 | 233185 | 144241 | 129281 | 140900 | 120385 | 113525 | 94826 | 90857 | 73670 | 296 |
Supernova results
| Analysis_ID | 95-39695.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 |