TB-Profiler result

Run: ERR108438

Summary

Run ID: ERR108438

Sample name:

Date: 31-03-2023 11:17:40

Number of reads: 4336697

Percentage reads mapped: 99.47

Strain: lineage4.3.3;lineage4.2.1;lineage2.2.1

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.75
lineage4.3 Euro-American (LAM) mainly-LAM None 0.65
lineage4.2 Euro-American H;T;LAM None 0.07
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.26
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.06
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.63
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 761109 p.Asp435Tyr missense_variant 0.59 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.28 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.18 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.62 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
eis 2715369 c.-37G>T upstream_gene_variant 0.32 kanamycin
embB 4247431 p.Met306Ile missense_variant 0.7 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.27 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.16 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 8040 p.Gly247Ser missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.24
mshA 575907 p.Ala187Val missense_variant 0.31
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.24
rpoC 764995 c.1626C>G synonymous_variant 0.66
rpoC 766645 p.Glu1092Asp missense_variant 0.32
rpoC 766667 p.Ser1100Ala missense_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.29
mmpL5 776182 p.Asp767Asn missense_variant 0.28
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.32
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918681 p.Asp248Cys missense_variant 0.58
katG 2154724 p.Arg463Leu missense_variant 0.36
PPE35 2167926 p.Leu896Ser missense_variant 0.19
PPE35 2169320 p.Leu431Phe missense_variant 0.31
PPE35 2169879 p.Phe245Cys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.21
kasA 2518919 p.Gly269Ser missense_variant 0.63
pepQ 2860571 c.-153T>G upstream_gene_variant 0.61
ribD 2987307 p.Ala157Pro missense_variant 0.15
thyA 3073806 c.666C>G synonymous_variant 0.32
thyA 3073868 p.Thr202Ala missense_variant 0.73
ald 3086742 c.-78A>C upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 0.64
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 0.62
clpC1 4038857 c.1848C>A synonymous_variant 0.24
embC 4242425 p.Arg855Gly missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.4
embA 4244823 p.Val531Leu missense_variant 0.55
embB 4248316 c.1803C>T synonymous_variant 0.62
embB 4249594 c.3081G>A synonymous_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 0.26
whiB6 4338563 c.-42G>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.23
gid 4407877 p.Gly109Ala missense_variant 0.73
gid 4407927 p.Glu92Asp missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 0.7