Detailed view of 4512-JFI-0506

Strain

ID 10
Name F344/NHsd
Type Inbred
Living False
Source Envigo
Note

Animal

Animal_name F344/NHsd_Rat1
Sex M
Age adolescent
Generation
Euthanasia_date 2018-02-01
Source Envigo
Note UTHSC order 6491, foundation stock

Tissue

ID 4512-JFI-0499
Type spleen
Transfer_History Chen to HudsonAlpha
Note None

Sequencing

DNA_source 4512-JFI-0499
Platform 10X Chromium
DNA_extraction_method HMW
DNA_concentration 62.8
DNA_target_length
DNA_extraction_facility HudsonAlpha
Library_kit 150bp_PE
Library_facility HudsonAlpha
Sequencing_instrument HiSeq_X10
Sequencing_date 2018-07-18
Sequencing_facility HudsonAlpha
Sequencing_notes Lanes per sample: 1
Raw_data_dir_name 4512-JFI-0506
Raw_data_format fastq.gz
Raw_data_file_size_GB 75
Raw_data_available_from Chen
Note None

Analysis

Analysis_ID 4512-JFI-0506.LR1 4512-JFI-0506.DV1
Software_name LongRanger DeepVariant
Software_version 2.2.2 0.9.0-gpu
Results_dir longranger_results/0506_f344nhsd /data/10_TB/deepvar
Analysis_date 2018-08-07 2019-12-04
Note

LongRanger results

Analysis_ID 4512-JFI-0506.LR1
instrument_ids E00438
gems_detected 1529109
mean_dna_per_gem 611751.8654
bc_on_whitelist 0.8591841644
bc_mean_qscore 38.42979635
n50_linked_reads_per_molecule 9
corrected_loaded_mass_ng 1.439070025
snps_phased 0.869223971
genes_phased_lt_100kb 0.7109217313
longest_phase_block 532529
n50_phase_block 46229
molecule_length_mean 25755.96485
molecule_length_stddev 41150.83578
number_reads 815667354
median_insert_size 329
mean_depth 34.72461418
zero_coverage 0.02607743548
mapped_reads 0.9140942645
pcr_duplication 0.03945994316
on_target_bases
r1_q20_bases_fract 0.9246434974
r1_q30_bases_fract 0.8520002895
r2_q20_bases_fract 0.8117106229
r2_q30_bases_fract 0.6822898412
si_q20_bases_fract 0.9631410233
si_q30_bases_fract 0.9375615366
bc_q20_bases_fract 0.9930208522
bc_q30_bases_fract 0.9806546775
large_sv_calls 1919
short_deletion_calls 32718

Deepvariant results

index 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176
Analysis_ID 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.DV1 4512-JFI-0506.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 49158 36108 32778 48658 53131 42882 41424 46032 35563 30132 102480 31425 117086 75473 74613 83945 62117 65152 56669 46978 45229 136
Biallelic_Insertion 49586 35760 30401 47886 51308 42908 39558 43371 35224 28695 102210 29885 113614 74654 73059 80425 61747 63475 55704 47045 42097 238
Biallelic_SNP 175150 160088 117295 200707 247047 174467 170785 191690 131098 112356 427195 129139 585450 311124 314859 357228 259714 304792 221040 175757 135659 830
Multiallelic_Complex 1476 798 834 1071 1195 956 943 1049 790 789 2784 685 2667 1824 1631 1874 1372 1578 1413 1232 522 4
Multiallelic_Deletion 2872 1656 1593 2054 2354 1688 1725 2182 1533 1384 4751 1224 5287 3661 3568 4037 2687 3267 2826 1850 876 3
Multiallelic_Insertion 4632 2833 2614 3354 4081 2852 2871 3763 2528 2260 7775 2209 8895 6169 5762 6763 4615 5650 4773 3048 1390 3
Multiallelic_SNP 94 67 163 75 140 148 84 148 73 207 382 144 400 211 123 151 333 231 121 186 94 21001
RefCall 344880 249371 215960 317900 336473 310187 265539 295921 238439 228530 824635 199430 795477 525244 498705 514452 457271 447584 383755 347638 306053 478
Transition 113442 101069 74750 117492 155148 105715 107855 123365 83988 70982 262438 82568 359427 195022 197460 223410 158002 193595 142111 106838 74668 352
Transversion 61708 59019 42545 83215 91899 68752 62930 68325 47110 41374 164757 46571 226023 116102 117399 133818 101712 111197 78929 68919 60991

Supernova results