TB-Profiler result

Run: SRR10303343

Summary

Run ID: SRR10303343

Sample name:

Date: 02-04-2023 16:43:39

Number of reads: 3137985

Percentage reads mapped: 99.54

Strain: lineage4.3.2.1;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 0.79
lineage4 Euro-American LAM;T;S;X;H None 0.17
lineage4.3 Euro-American (LAM) mainly-LAM None 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.84
lineage4.3.2 Euro-American (LAM) LAM3 None 0.17
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.84
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.14
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 0.81 streptomycin
rpsL 781821 p.Lys88Gln missense_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 0.8 pyrazinamide
pncA 2288955 p.Lys96Thr missense_variant 0.14 pyrazinamide
embB 4246734 p.Leu74Arg missense_variant 0.87 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.12 ethambutol
embB 4247496 p.Asp328Gly missense_variant 0.85 ethambutol
ethA 4326426 c.1047delT frameshift_variant 0.99 ethionamide, 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 5520 p.Pro94Leu missense_variant 0.23
gyrA 7222 c.-80C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.82
mshA 575907 p.Ala187Val missense_variant 0.78
mshA 576108 p.Ala254Gly missense_variant 0.39
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoB 761004 p.Thr400Gly missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.81
rpoC 764995 c.1626C>G synonymous_variant 0.18
rpoC 766645 p.Glu1092Asp missense_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.78
mmpL5 776182 p.Asp767Asn missense_variant 0.79
mmpR5 779120 p.Leu44Pro missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2170065 p.Ala183Gly missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290107 c.-866T>A upstream_gene_variant 0.2
Rv2752c 3064974 p.Asn406Lys missense_variant 0.87
thyA 3073868 p.Thr202Ala missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.79
fbiA 3640407 c.-136G>A upstream_gene_variant 0.17
rpoA 3878613 c.-106A>C upstream_gene_variant 0.3
rpoA 3878637 c.-130G>C upstream_gene_variant 0.19
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.84
embB 4246584 p.Arg24Pro missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.77
gid 4407927 p.Glu92Asp missense_variant 0.78
gid 4408156 p.Leu16Arg missense_variant 0.24