Detailed view of 95-39697
Strain
| ID | 36 |
|---|---|
| Name | ACI/N |
| Type | Inbred |
| Living | False |
| Source | |
| Note | HS founder |
Animal
| Animal_name | ACI/N_rat1 |
|---|---|
| Sex | M |
| Age | adult |
| Generation | None |
| Euthanasia_date | None |
| Source | Mandel |
| Note | None |
Tissue
| ID | 95-38314 |
|---|---|
| Type | tail |
| Transfer_History | Mandel to Dalgard |
| Note | None |
Sequencing
| DNA_source | 95-38314 |
|---|---|
| Platform | 10X Chromium |
| DNA_extraction_method | HMW |
| DNA_concentration | |
| DNA_target_length | |
| DNA_extraction_facility | USUHS |
| Library_kit | 150bp_PE |
| Library_facility | USUHS |
| Sequencing_instrument | HiSeq_X |
| Sequencing_date | 2019-09-01 |
| Sequencing_facility | USUHS |
| Sequencing_notes | |
| Raw_data_dir_name | 95-39697 |
| Raw_data_format | fastq.gz |
| Raw_data_file_size_GB | 58 |
| Raw_data_available_from | Chen |
| Note | None |
Analysis
| Analysis_ID | 95-39697.LR1 | 95-39697.GH1 | 95-39697.DV1 |
|---|---|---|---|
| Software_name | LongRanger | GROC-SVs | DeepVariant |
| Software_version | 2.2.2 | Udit_PR3 | 0.9.0-gpu |
| Results_dir | longranger_results/ACI-N | grocsvs_HXB | /data/10_TB/deepvar |
| Analysis_date | 2019-10-08 | 2020-03-02 | 2019-12-04 |
| Note | combined analysis of BN samples and HXB |
LongRanger results
| Analysis_ID | 95-39697.LR1 |
|---|---|
| instrument_ids | A00735 |
| gems_detected | 1749193 |
| mean_dna_per_gem | 615124.9917 |
| bc_on_whitelist | 0.9316551375 |
| bc_mean_qscore | 36.31525456 |
| n50_linked_reads_per_molecule | 14 |
| corrected_loaded_mass_ng | 1.447004884 |
| snps_phased | 0.9248818289 |
| genes_phased_lt_100kb | 0.8171724648 |
| longest_phase_block | 678438 |
| n50_phase_block | 42883 |
| molecule_length_mean | 40364.91036 |
| molecule_length_stddev | 37814.69299 |
| number_reads | 793816770 |
| median_insert_size | 349 |
| mean_depth | 35.91365756 |
| zero_coverage | 0.03586707308 |
| mapped_reads | 0.9433336562 |
| pcr_duplication | 0.04056157693 |
| on_target_bases | |
| r1_q20_bases_fract | 0.9507738979 |
| r1_q30_bases_fract | 0.9045488832 |
| r2_q20_bases_fract | 0.935844973 |
| r2_q30_bases_fract | 0.8803611808 |
| si_q20_bases_fract | NaN |
| si_q30_bases_fract | NaN |
| bc_q20_bases_fract | 0.986088115 |
| bc_q30_bases_fract | 0.9595697174 |
| large_sv_calls | 2091 |
| short_deletion_calls | 20191 |
Deepvariant results
| index |
|---|
| Analysis_ID |
| Chr |
| Biallelic_Deletion |
| Biallelic_Insertion |
| Biallelic_SNP |
| Multiallelic_Complex |
| Multiallelic_Deletion |
| Multiallelic_Insertion |
| Multiallelic_SNP |
| RefCall |
| Transition |
| Transversion |