TB-Profiler result

Run: SRR5527200

Summary

Run ID: SRR5527200

Sample name:

Date: 04-04-2023 10:36:52

Number of reads: 575933

Percentage reads mapped: 99.62

Strain: lineage2.2.1.1

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 1.0
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 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 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759746 c.-61C>G upstream_gene_variant 0.12
rpoB 761118 p.Asn438Asp missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764027 p.Glu220* stop_gained 0.14
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766533 p.Leu1055Pro missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781501 c.-59C>G upstream_gene_variant 0.11
fbiC 1303842 c.912C>T synonymous_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170440 p.Gln58Pro missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518398 p.Trp95Leu missense_variant 0.11
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2519365 c.1251A>G stop_lost&splice_region_variant 0.1
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2747486 p.Trp38* stop_gained 0.17
folC 2747776 c.-178G>T upstream_gene_variant 0.12
Rv2752c 3065000 p.Gly398Arg missense_variant 0.11
thyA 3074313 c.159A>G synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339349 p.Asp78Asn missense_variant 0.12
Rv3083 3448319 c.-185C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613255 c.-139G>A upstream_gene_variant 0.11
fbiB 3642473 p.Met313Ile missense_variant 0.2
clpC1 4040228 c.477G>A synonymous_variant 0.13
embC 4242255 p.Pro798Arg missense_variant 0.15
embC 4242557 p.Gln899Lys missense_variant 0.25
embC 4242632 p.Pro924Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248558 p.Tyr682Ser missense_variant 0.13
aftB 4267645 p.Asp398His missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327589 p.Gly14Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0