Detailed view of 95-39677
Strain
| ID | 73 |
|---|---|
| Name | HXB4 |
| Type | RI |
| Living | False |
| Source | |
| Note |
Animal
| Animal_name | HXB4_Rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | |
| Euthanasia_date | 2018-08-01 |
| Source | Pravenec |
| Note |
Tissue
| ID | 4512-JFI-0522 |
|---|---|
| Type | spleen |
| Transfer_History | Pravenec to Chen to HudsonAlpha |
| Note | None |
Sequencing
| DNA_source | 4512-JFI-0522 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | 32.6 |
| 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 | 95-39677 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 142 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39677.LR1 | 95-39677.SN1 | 95-39677.GH1 | 95-39677.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/HXB4 | supernova_results/HXB4 | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-22 | 2020-02-15 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39677.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1563410 |
| mean_dna_per_gem | 740374.2766 |
| bc_on_whitelist | 0.9293977937 |
| bc_mean_qscore | 36.33070871 |
| n50_linked_reads_per_molecule | 35 |
| corrected_loaded_mass_ng | 1.741638218 |
| snps_phased | 0.8904670955 |
| genes_phased_lt_100kb | 0.9130848231 |
| longest_phase_block | 2477391 |
| n50_phase_block | 254708 |
| molecule_length_mean | 39053.10964 |
| molecule_length_stddev | 62032.9653 |
| number_reads | 1994082726 |
| median_insert_size | 334 |
| mean_depth | 91.46057916 |
| zero_coverage | 0.02005486137 |
| mapped_reads | 0.9513840872 |
| pcr_duplication | 0.08943090761 |
| on_target_bases | |
| r1_q20_bases_fract | 0.955740675 |
| r1_q30_bases_fract | 0.9121580016 |
| r2_q20_bases_fract | 0.944987551 |
| r2_q30_bases_fract | 0.8933311798 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.9863489565 |
| bc_q30_bases_fract | 0.9608331881 |
| large_sv_calls | 2660 |
| short_deletion_calls | 40045 |
Deepvariant results
| index | 947 | 948 | 949 | 950 | 951 | 952 | 953 | 954 | 955 | 956 | 957 | 958 | 959 | 960 | 961 | 962 | 963 | 964 | 965 | 966 | 967 | 968 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Analysis_ID | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.DV1 | 95-39677.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 | 52316 | 20250 | 33412 | 49425 | 46268 | 44100 | 33875 | 35967 | 36452 | 27995 | 117384 | 27126 | 92191 | 47810 | 68820 | 62954 | 59318 | 56567 | 42235 | 33868 | 56199 | 381 |
| Biallelic_Insertion | 47155 | 19426 | 28675 | 43931 | 41371 | 39770 | 29963 | 31940 | 32481 | 24242 | 104244 | 23941 | 83373 | 43774 | 61539 | 56321 | 53383 | 50808 | 38363 | 30569 | 49840 | 481 |
| Biallelic_SNP | 199849 | 40232 | 125137 | 207323 | 197554 | 198480 | 111741 | 115394 | 142332 | 103689 | 561223 | 91195 | 381359 | 107298 | 276617 | 197901 | 229838 | 255620 | 119636 | 84302 | 164408 | 2937 |
| Multiallelic_Complex | 1229 | 395 | 700 | 856 | 874 | 886 | 597 | 688 | 668 | 552 | 2597 | 533 | 1892 | 877 | 1320 | 1043 | 1128 | 1345 | 893 | 687 | 952 | 15 |
| Multiallelic_Deletion | 2896 | 422 | 1386 | 1875 | 1739 | 1538 | 1049 | 1088 | 1492 | 1052 | 5402 | 816 | 3298 | 1107 | 2761 | 1877 | 2131 | 2458 | 1525 | 781 | 1915 | 38 |
| Multiallelic_Insertion | 5154 | 736 | 2695 | 3381 | 3078 | 2610 | 1831 | 2051 | 2561 | 1886 | 9434 | 1598 | 5790 | 2063 | 4790 | 3335 | 4001 | 4297 | 2568 | 1327 | 3380 | 57 |
| Multiallelic_SNP | 104 | 28 | 136 | 87 | 135 | 135 | 73 | 104 | 59 | 185 | 467 | 25 | 252 | 45 | 106 | 87 | 168 | 247 | 99 | 161 | 96 | 28650 |
| RefCall | 235866 | 136598 | 174504 | 214671 | 225667 | 228506 | 171776 | 189215 | 156259 | 168735 | 656452 | 127971 | 518287 | 297580 | 313838 | 310065 | 281391 | 322300 | 240474 | 235615 | 434562 | 1575 |
| Transition | 129848 | 21186 | 79164 | 119938 | 122295 | 119665 | 67443 | 71618 | 90045 | 63740 | 346715 | 56743 | 228198 | 59320 | 170844 | 115425 | 138490 | 157324 | 72781 | 45399 | 89003 | 1362 |
| Transversion | 70001 | 19046 | 45973 | 87385 | 75259 | 78815 | 44298 | 43776 | 52287 | 39949 | 214508 | 34452 | 153161 | 47978 | 105773 | 82476 | 91348 | 98296 | 46855 | 38903 | 75405 |
Supernova results
| Analysis_ID | 95-39677.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 |