Detailed view of 95-39688
Strain
| ID | 66 |
|---|---|
| Name | HXB23 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB23_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0533 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0533 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 32 |
| 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 | 95-39688 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 91 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39688.LR1 | 95-39688.SN1 | 95-39688.GH1 | 95-39688.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/HXB23 | supernova_results/HXB23 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-08 | 2020-01-26 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39688.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1797437 |
| mean_dna_per_gem | 735292.5292 |
| bc_on_whitelist | 0.9203770328 |
| bc_mean_qscore | 36.44360707 |
| n50_linked_reads_per_molecule | 9 |
| corrected_loaded_mass_ng | 1.72968404 |
| snps_phased | 0.8895348686 |
| genes_phased_lt_100kb | 0.7804576376 |
| longest_phase_block | 1506577 |
| n50_phase_block | 57342 |
| molecule_length_mean | 21579.44908 |
| molecule_length_stddev | 53311.35773 |
| number_reads | 1306291736 |
| median_insert_size | 289 |
| mean_depth | 58.43606424 |
| zero_coverage | 0.02078360365 |
| mapped_reads | 0.9402017698 |
| pcr_duplication | 0.05302942663 |
| on_target_bases | |
| r1_q20_bases_fract | 0.951814003 |
| r1_q30_bases_fract | 0.9088091366 |
| r2_q20_bases_fract | 0.9376563399 |
| r2_q30_bases_fract | 0.8865642914 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9888153352 |
| bc_q30_bases_fract | 0.967304954 |
| large_sv_calls | 1934 |
| short_deletion_calls | 28657 |
Deepvariant results
| index | 771 | 772 | 773 | 774 | 775 | 776 | 777 | 778 | 779 | 780 | 781 | 782 | 783 | 784 | 785 | 786 | 787 | 788 | 789 | 790 | 791 | 792 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.DV1 | 95-39688.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 | 42588 | 20395 | 32302 | 44691 | 48983 | 35789 | 29029 | 34862 | 33436 | 23703 | 83364 | 20245 | 85688 | 44949 | 65796 | 74375 | 61093 | 51116 | 43199 | 38728 | 51435 | 418 |
| Biallelic_Insertion | 40459 | 20198 | 28476 | 41081 | 44879 | 33678 | 26610 | 31745 | 30575 | 21686 | 78559 | 19192 | 80485 | 43508 | 60605 | 67994 | 56239 | 48307 | 40852 | 35932 | 49156 | 597 |
| Biallelic_SNP | 134281 | 39004 | 120576 | 175244 | 220737 | 126663 | 73880 | 107095 | 114829 | 67472 | 283172 | 37584 | 339423 | 94236 | 258104 | 290831 | 262918 | 208221 | 136896 | 109479 | 134790 | 2796 |
| Multiallelic_Complex | 1121 | 459 | 784 | 949 | 1070 | 789 | 569 | 735 | 692 | 565 | 2080 | 420 | 1932 | 953 | 1540 | 1605 | 1454 | 1311 | 1033 | 874 | 932 | 18 |
| Multiallelic_Deletion | 1966 | 507 | 1312 | 1595 | 1844 | 1024 | 677 | 1190 | 1283 | 771 | 2731 | 364 | 2797 | 914 | 2721 | 2736 | 2310 | 1957 | 1504 | 1186 | 1592 | 35 |
| Multiallelic_Insertion | 3932 | 967 | 2585 | 2966 | 3504 | 1863 | 1399 | 2248 | 2408 | 1478 | 5407 | 925 | 5402 | 1883 | 4928 | 5305 | 4570 | 3852 | 3002 | 2280 | 2796 | 56 |
| Multiallelic_SNP | 70 | 35 | 135 | 85 | 142 | 116 | 67 | 98 | 60 | 86 | 242 | 24 | 255 | 101 | 93 | 146 | 324 | 165 | 97 | 118 | 94 | 2 |
| RefCall | 261228 | 167456 | 182516 | 247884 | 271075 | 249190 | 191481 | 220905 | 182448 | 177726 | 660280 | 131844 | 591754 | 360350 | 379249 | 395821 | 397922 | 356957 | 283810 | 272120 | 474446 | 27931 |
| Transition | 85363 | 21053 | 76092 | 98091 | 136232 | 73652 | 42983 | 67213 | 72601 | 40392 | 166291 | 20848 | 201498 | 49437 | 159176 | 177669 | 157719 | 126285 | 81882 | 64471 | 71362 | 1468 |
| Transversion | 48918 | 17951 | 44484 | 77153 | 84505 | 53011 | 30897 | 39882 | 42228 | 27080 | 116881 | 16736 | 137925 | 44799 | 98928 | 113162 | 105199 | 81936 | 55014 | 45008 | 63428 | 1328 |
Supernova results
| Analysis_ID | 95-39688.SN1 |
|---|---|
| assembly_size | 2442331848 |
| barcode_fraction | 1 |
| bases_per_read | 137.512 |
| bridge_1_50 | 181.563 |
| bridge_50 | 0.011 |
| bridge_model_badness_of_fit | 1.05454 |
| checksum | 7.317902656833545e+18 |
| contig_N50 | 33642 |
| dinucleotide_percent | 1.325 |
| dup_perc | 16.7191 |
| edge_N50 | 7319 |
| effective_coverage | 44.2226 |
| est_genome_size | 3170000000 |
| gc_percent | 42.0094 |
| hetdist | 34611 |
| high_AT_index | 0.0747524 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 18952.2 |
| m10 | 2.53164 |
| median_ins_sz | 306 |
| nreads | 1306291736 |
| p10 | 22.2941 |
| phase_block_N50 | 19380 |
| placed_perc | 61.1097 |
| proper_pairs_perc | 91.8509 |
| q30_r2_perc | 88.6564 |
| raw_coverage | 61.4117 |
| read_rate_DF_1_threaded | 21.9207 |
| read_rate_IO_10_threaded | 2623.56 |
| read_rate_IO_1_threaded | 3182.82 |
| repfrac | 10.9507 |
| rpb_N50 | 890 |
| scaffold_N50 | 1630182 |
| scaffolds_10kb_plus | 6604 |
| scaffolds_1kb_plus | 34082 |
| unbar_perc | 7.9623 |
| valid_bc_perc | 92.0377 |