TB-Profiler result

Run: ERR4831827

Summary

Run ID: ERR4831827

Sample name:

Date: 20-10-2023 13:00:25

Number of reads: 1941687

Percentage reads mapped: 99.45

Strain: lineage2.2.1;lineage1.1.1.1

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 (0.51)
Isoniazid R katG p.Ser315Thr (0.58)
Ethambutol R embB p.Met306Ile (0.63)
Pyrazinamide R pncA c.289_290dupGG (0.50)
Streptomycin R rpsL p.Lys43Arg (0.50)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.110delA (0.53), ethA c.110delA (0.53)
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 0.58
lineage1 Indo-Oceanic EAI RD239 0.48
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.48
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.56
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.57
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.44
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.45
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 0.51 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid
pncA 2288951 c.289_290dupGG frameshift_variant 0.5 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.63 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.53 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
gyrB 6112 p.Met291Ile missense_variant 0.48
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.46
gyrA 9143 c.1842T>C synonymous_variant 0.42
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.47
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.55
ccsA 620625 p.Ile245Met missense_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.51
rpoC 763886 c.517C>A synonymous_variant 0.53
rpoC 765171 p.Pro601Leu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.53
mmpL5 777581 p.Tyr300* stop_gained 0.36
mmpL5 777745 p.Gly246Ser missense_variant 0.59
mmpS5 779615 c.-710C>G upstream_gene_variant 0.46
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.5
embR 1417019 p.Cys110Tyr missense_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.62
rpsA 1834177 c.636A>C synonymous_variant 0.55
rpsA 1834319 p.Val260Ile missense_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155077 p.Lys345Asn missense_variant 0.43
katG 2156389 c.-278G>C upstream_gene_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.42
PPE35 2169432 p.Pro394Leu missense_variant 0.34
Rv1979c 2222092 p.Ser358Leu missense_variant 0.43
Rv1979c 2222308 p.Asp286Gly missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.35
ahpC 2726051 c.-142G>A upstream_gene_variant 0.39
Rv2752c 3064632 c.1560C>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.33
fprA 3475159 p.Asn385Asp missense_variant 0.39
Rv3236c 3612813 p.Thr102Ala missense_variant 0.53
rpoA 3878417 p.Gly31Cys missense_variant 0.53
ddn 3986813 c.-31T>C upstream_gene_variant 0.42
clpC1 4040517 p.Val63Ala missense_variant 0.48
embC 4241042 p.Asn394Asp missense_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.51
embA 4243848 p.Val206Met missense_variant 0.48
embA 4244096 c.864C>T synonymous_variant 0.51
embA 4245969 p.Pro913Ser missense_variant 0.42
embB 4247646 p.Glu378Ala missense_variant 0.41
aftB 4267647 p.Asp397Gly missense_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 0.49
aftB 4269606 c.-770T>C upstream_gene_variant 0.48
whiB6 4338242 p.Gln94Glu missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.41
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.35
gid 4407927 p.Glu92Asp missense_variant 0.64