TB-Profiler result

Run: SRR5709818
Summary

Run ID: SRR5709818

Sample name:

Date: 20-10-2023 16:37:25

Number of reads: 1701893

Percentage reads mapped: 99.55

Strain: lineage2.2.1;lineage1.2.1.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.65)
Isoniazid R katG p.Ser315Thr (0.78)
Ethambutol R embB p.Gly406Asp (0.84)
Pyrazinamide R pncA p.Ile31Thr (0.73)
Streptomycin R rpsL p.Lys43Arg (0.83)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.639_640delGT (0.78), ethA c.639_640delGT (0.78)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.73
lineage1 Indo-Oceanic EAI RD239 0.24
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.75
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.76
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.22
lineage1.2.1.2 Indo-Oceanic NA RD239 0.26
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761155 p.Ser450Leu missense_variant 0.65 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid
pncA 2289150 p.Ile31Thr missense_variant 0.73 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.84 ethambutol
ethA 4326833 c.639_640delGT frameshift_variant 0.78 ethionamide, ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.19
gyrA 9143 c.1842T>C synonymous_variant 0.31
gyrA 9260 c.1959G>C synonymous_variant 0.26
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 0.32
mshA 575907 p.Ala187Val missense_variant 0.71
ccsA 620625 p.Ile245Met missense_variant 0.72
rpoB 761998 p.Leu731Pro missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.19
rpoC 763884 p.Ala172Val missense_variant 0.34
rpoC 763886 c.517C>A synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.89
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303312 p.Ile128Val missense_variant 0.82
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 0.31
rpsA 1834177 c.636A>C synonymous_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.29
kasA 2519048 p.Gly312Ser missense_variant 0.28
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77
clpC1 4040517 p.Val63Ala missense_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 0.29
embC 4241042 p.Asn394Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.8
embA 4243580 c.348G>A synonymous_variant 0.22
embA 4244420 c.1188G>C synonymous_variant 0.27
embA 4245969 p.Pro913Ser missense_variant 0.3
embB 4247578 c.1065G>A synonymous_variant 0.24
aftB 4267435 p.Pro468Ser missense_variant 0.75
aftB 4267647 p.Asp397Gly missense_variant 0.72
ubiA 4269387 p.Glu149Asp missense_variant 0.22
aftB 4269606 c.-770T>C upstream_gene_variant 0.16
whiB6 4338361 p.Arg54Gln missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.26
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 0.76