TGS-TB

Strain	Raw reads	After quality trimming	Removal of excess reads (target: 100×)	Mapped reads	H37Rv reference genome (NC_000962.3) 4,411,532 bp
Strain	Raw reads	After quality trimming	Removal of excess reads (target: 100×)	Mapped reads	Covered region	Avg. depth
Strain_A	1,547,940	1,343,742	1,343,742	1,337,869	4,375,571	64.3×
Strain_A		86.81%	86.81%	86.43%	99.18%
Strain_B	1,092,148	1,017,728	1,017,728	1,012,408	4,386,485	55.1×
Strain_B		93.19%	93.19%	92.70%	99.43%
Strain_C	3,966,344	3,634,288	2,083,926	2,068,591	4,370,066	109.4×
Strain_C		91.63%	52.54%	52.15%	99.06%
Strain_D	3,473,398	3,343,440	2,136,823	2,125,800	4,371,932	109.3×
Strain_D		96.26%	61.52%	61.20%	99.10%

Completed in silico genotyping

Potential AMR prediction
KvarQ MTBC analysis
(Lineage / Antimicrobial Resistance)
version: MTBC.niid.3.20150403
TBprofiler
Core-genome phylogeny
- ML Tree by RAxML with bootstrap test 100 times
  - in Newick format (7.1KB)
  - in PDF format (8.4KB)
- Linkage Network analysis (for PopART)
  - Only queries in NEXUS format (6.4KB)
  - Queries with 78 references in NEXUS format (1.8MB)
- SNVs raw data
  - in tabular format (810KB)
  - in multi fasta format (1.8MB)
  - in pairwize SNV matrix (37KB)

SNV data without reference data in fasta format. (Minumum spanning tree can be made by using PHYLOViZ.) (6.2 KBytes)

SNV data for only queries in NEXUS format. (Minumum spanning tree can be made by using PopART.) (6.3 KBytes)

SNV data with reference data in NEXUS format. (Minumum spanning tree can be made by using PopART.) (1.7 MBytes)