TB-Profiler result

Run: ERR4797716
Summary

Run ID: ERR4797716

Sample name:

Date: 01-04-2023 07:51:19

Number of reads: 3331584

Percentage reads mapped: 99.47

Strain: lineage4;lineage1.1.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 0.09
lineage1 Indo-Oceanic EAI RD239 0.93
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.91
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 761095 p.Leu430Pro missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.1 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.95 isoniazid, 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 0.9
gyrB 6124 c.885C>T synonymous_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 8452 p.Ala384Val missense_variant 0.92
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 0.95
fgd1 491742 c.960T>C synonymous_variant 0.93
rpoB 761461 p.Arg552His missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.89
PPE35 2167926 p.Leu896Ser missense_variant 0.92
PPE35 2167983 p.Gly877Asp missense_variant 0.91
Rv1979c 2222308 p.Asp286Gly missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.93
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
fprA 3474597 c.591C>A synonymous_variant 0.94
fprA 3474700 p.Gly232Ser missense_variant 0.94
fprA 3475159 p.Asn385Asp missense_variant 0.96
rpoA 3878630 c.-123G>C upstream_gene_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.89
embC 4239921 p.Arg20Leu missense_variant 0.94
embC 4240671 p.Thr270Ile missense_variant 0.95
embC 4241042 p.Asn394Asp missense_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.87
embA 4245969 p.Pro913Ser missense_variant 0.91
embB 4247646 p.Glu378Ala missense_variant 0.92
embB 4249673 p.Ser1054Pro missense_variant 0.94
ubiA 4269387 p.Glu149Asp missense_variant 0.96
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.96
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.82
gid 4407935 p.Leu90Val missense_variant 0.88
gid 4407944 p.Gln87Glu missense_variant 0.91