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TGS-TB

An outbreak case

Strain Raw reads After
quality trimming
Removal of
excess reads
(target: 100×)
Mapped reads H37Rv reference genome
(NC_000962.3)
4,411,532 bp
Covered region Avg. depth
JP01_S1_L001 1,971,600 1,833,796 1,833,796 1,825,763 4,357,346 75.2×
93.01% 93.01% 92.60% 98.77%
JP02_S2_L001 2,449,108 2,280,960 2,280,960 2,270,388 4,359,611 90.9×
93.13% 93.13% 92.70% 98.82%
JP03_S3_L001 3,586,484 3,303,150 2,682,756 2,672,120 4,359,143 106.6×
92.10% 74.80% 74.51% 98.81%
JP04_S4_L001 4,615,212 4,255,652 2,619,703 2,608,457 4,358,675 105.9×
92.21% 56.76% 56.52% 98.80%
JP05_S5_L001 2,916,864 2,629,104 2,629,104 2,619,289 4,356,600 106.4×
90.13% 90.13% 89.80% 98.75%
JP06_S6_L001 2,941,708 2,631,996 2,631,996 2,622,607 4,353,900 107.1×
89.47% 89.47% 89.15% 98.69%
JP07_S7_L001 2,436,346 2,142,480 2,142,480 2,132,563 4,345,476 74.7×
87.94% 87.94% 87.53% 98.50%

Reads trimming report

SNV detection report

Number of SNVs
SNV sites Original Effective
Original dataset 21,805 20,928 95.98%
Additional - 219
Total 21,147

Completed in silico genotyping


SNV data without reference data in fasta format. (Minumum spanning tree can be made by using PHYLOViZ.) (147 Bytes)
SNV data for only queries in NEXUS format. (Minumum spanning tree can be made by using PopART.) (244 Bytes)
SNV data with reference data in NEXUS format. (Minumum spanning tree can be made by using PopART.) (1.7 MBytes)

Phylocore genome tree