Detailed view of 95-39685
Strain
| ID | 63 |
|---|---|
| Name | HXB20 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB20_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0530 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0530 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 31.6 |
| 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 | 95-39685 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 91 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39685.LR1 | 95-39685.SN1 | 95-39685.GH1 | 95-39685.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/HXB20 | supernova_results/HXB20 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-03 | 2020-01-28 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39685.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1586542 |
| mean_dna_per_gem | 707879.6353 |
| bc_on_whitelist | 0.9189714293 |
| bc_mean_qscore | 36.33077664 |
| n50_linked_reads_per_molecule | 20 |
| corrected_loaded_mass_ng | 1.665198624 |
| snps_phased | 0.8886369108 |
| genes_phased_lt_100kb | 0.8710928035 |
| longest_phase_block | 1557237 |
| n50_phase_block | 104141 |
| molecule_length_mean | 34211.27381 |
| molecule_length_stddev | 48871.51692 |
| number_reads | 1273104106 |
| median_insert_size | 300 |
| mean_depth | 57.89216311 |
| zero_coverage | 0.0208777579 |
| mapped_reads | 0.9470339514 |
| pcr_duplication | 0.05152632273 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9526891355 |
| r1_q30_bases_fract | 0.9078633826 |
| r2_q20_bases_fract | 0.9410948174 |
| r2_q30_bases_fract | 0.8886018568 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863197062 |
| bc_q30_bases_fract | 0.9608743123 |
| large_sv_calls | 2486 |
| short_deletion_calls | 30302 |
Deepvariant results
| index | 705 | 706 | 707 | 708 | 709 | 710 | 711 | 712 | 713 | 714 | 715 | 716 | 717 | 718 | 719 | 720 | 721 | 722 | 723 | 724 | 725 | 726 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.DV1 | 95-39685.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 | 29799 | 21004 | 20541 | 48459 | 40876 | 34046 | 36628 | 43282 | 32371 | 27941 | 68104 | 23994 | 79486 | 70605 | 59806 | 52846 | 41451 | 58151 | 37887 | 36442 | 51480 | 438 |
| Biallelic_Insertion | 29675 | 20657 | 18992 | 43906 | 37590 | 31566 | 33095 | 38155 | 29712 | 24767 | 64786 | 21963 | 74250 | 64024 | 54730 | 48849 | 39416 | 53196 | 35906 | 33780 | 47883 | 556 |
| Biallelic_SNP | 49232 | 45755 | 30690 | 196330 | 146917 | 109361 | 132866 | 166892 | 110070 | 100417 | 158862 | 69330 | 274500 | 270040 | 192788 | 110172 | 110813 | 257537 | 89052 | 102462 | 132102 | 2859 |
| Multiallelic_Complex | 761 | 433 | 389 | 991 | 769 | 738 | 698 | 932 | 587 | 629 | 1565 | 488 | 1701 | 1527 | 1236 | 992 | 890 | 1343 | 806 | 764 | 905 | 15 |
| Multiallelic_Deletion | 753 | 430 | 244 | 1776 | 1263 | 969 | 1113 | 1676 | 1051 | 952 | 1441 | 573 | 2192 | 2698 | 1913 | 1162 | 896 | 2410 | 1050 | 840 | 1480 | 22 |
| Multiallelic_Insertion | 1627 | 828 | 634 | 3253 | 2515 | 1666 | 2205 | 3119 | 2024 | 1850 | 2902 | 1214 | 4190 | 4953 | 3803 | 2319 | 1757 | 4430 | 2075 | 1655 | 2490 | 61 |
| Multiallelic_SNP | 35 | 32 | 37 | 89 | 85 | 99 | 94 | 99 | 55 | 156 | 202 | 20 | 206 | 113 | 78 | 48 | 248 | 211 | 58 | 155 | 89 | 2 |
| RefCall | 231673 | 167025 | 152039 | 255651 | 243961 | 245729 | 205456 | 233246 | 179982 | 187014 | 615821 | 140689 | 576871 | 400124 | 360611 | 346875 | 358914 | 364367 | 265495 | 271168 | 468740 | 29677 |
| Transition | 27158 | 24436 | 14370 | 113260 | 87108 | 64286 | 81291 | 105998 | 67965 | 61263 | 84290 | 41355 | 161029 | 166885 | 117062 | 62099 | 58764 | 158444 | 51096 | 57367 | 70180 | 1494 |
| Transversion | 22074 | 21319 | 16320 | 83070 | 59809 | 45075 | 51575 | 60894 | 42105 | 39154 | 74572 | 27975 | 113471 | 103155 | 75726 | 48073 | 52049 | 99093 | 37956 | 45095 | 61922 | 1365 |
Supernova results
| Analysis_ID | 95-39685.SN1 |
|---|---|
| assembly_size | 2478547958 |
| barcode_fraction | 1 |
| bases_per_read | 137.765 |
| bridge_1_50 | 27.484 |
| bridge_50 | 0.085 |
| bridge_model_badness_of_fit | 1.07146 |
| checksum | -6.45125e+18 |
| contig_N50 | 34765 |
| dinucleotide_percent | 1.14766 |
| dup_perc | 15.905 |
| edge_N50 | 7725 |
| effective_coverage | 46.7305 |
| est_genome_size | 2970000000 |
| gc_percent | 42.2061 |
| hetdist | 24707 |
| high_AT_index | 0.0739282 |
| likely_sequencers | NovaSeq |
| lw_mean_mol_len | 28784.5 |
| m10 | 2.94265 |
| median_ins_sz | 315 |
| nreads | 1273104106 |
| p10 | 60.9412 |
| phase_block_N50 | 94104 |
| placed_perc | 61.6629 |
| proper_pairs_perc | 92.5723 |
| q30_r2_perc | 88.8602 |
| raw_coverage | 64.0633 |
| read_rate_DF_1_threaded | 18.1441 |
| read_rate_IO_10_threaded | 2934.65 |
| read_rate_IO_1_threaded | 3720.73 |
| repfrac | 8.74861 |
| rpb_N50 | 898 |
| scaffold_N50 | 5072751 |
| scaffolds_10kb_plus | 7683 |
| scaffolds_1kb_plus | 40168 |
| unbar_perc | 8.10286 |
| valid_bc_perc | 91.8971 |