TB-Profiler result

Run: ERR1035059
Summary

Run ID: ERR1035059

Sample name:

Date: 31-03-2023 09:57:22

Number of reads: 3980825

Percentage reads mapped: 99.32

Strain: lineage4.1.1.3;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.86
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.1 Euro-American T;X;H None 0.14
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.09
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.11
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 0.74 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.76 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.87 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 0.93 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 0.85 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 0.78
rpoC 763555 c.186C>T synonymous_variant 0.82
rpoC 764670 p.Pro434Arg missense_variant 0.9
rpoC 767314 p.Tyr1315* stop_gained 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
mmpL5 776182 p.Asp767Asn missense_variant 0.79
mmpS5 778979 c.-74G>T upstream_gene_variant 0.84
mmpS5 779615 c.-710C>G upstream_gene_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.86
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.89
PPE35 2167926 p.Leu896Ser missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 0.85
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8
rpoA 3878647 c.-140delG upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 0.86
aftB 4267647 p.Asp397Gly missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.87
gid 4407798 c.405G>T synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 0.84