TB-Profiler result

Run: ERR234571
Summary

Run ID: ERR234571

Sample name:

Date: 31-03-2023 18:05:52

Number of reads: 3549331

Percentage reads mapped: 99.67

Strain: lineage4.4.1.1;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 0.18
lineage4 Euro-American LAM;T;S;X;H None 0.83
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage4.4 Euro-American S;T None 0.77
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.16
lineage4.4.1 Euro-American (S-type) S;T None 0.75
lineage4.4.1.1 Euro-American S;Orphans None 0.73
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 762089 p.Glu761Asp missense_variant 0.15 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.11 ethambutol
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 0.13
ccsA 619876 c.-15C>T upstream_gene_variant 0.65
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.19
rpoC 766645 p.Glu1092Asp missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.22
mmpL5 776182 p.Asp767Asn missense_variant 0.23
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.79
katG 2154724 p.Arg463Leu missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 0.15
PPE35 2169840 p.Gly258Asp missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.82
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
clpC1 4038857 c.1848C>A synonymous_variant 0.31
embC 4242425 p.Arg855Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.3
aftB 4267647 p.Asp397Gly missense_variant 0.23
ethA 4328376 c.-903G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.21