TB-Profiler result

Run: SRR18715333
Summary

Run ID: SRR18715333

Sample name:

Date: 03-04-2023 20:29:25

Number of reads: 4700309

Percentage reads mapped: 99.2

Strain: lineage4.2.1.1;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 0.86
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.2 Euro-American H;T;LAM None 0.16
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.83
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.18
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.15
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 761110 p.Asp435Val missense_variant 0.12 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.16 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.18 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.15 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 0.19 pyrazinamide
pncA 2288953 p.Gly97Ser missense_variant 0.28 pyrazinamide
pncA 2288961 p.Phe94Ser missense_variant 0.59 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.88 kanamycin
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.16 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 0.88
mshA 575907 p.Ala187Val missense_variant 0.87
mshA 576108 p.Ala254Gly missense_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 0.86
rpoB 762286 p.Arg827Leu missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 766376 p.Ile1003Val missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
mmpL5 776182 p.Asp767Asn missense_variant 0.85
mmpL5 776802 p.Met560Thr missense_variant 0.15
mmpL5 777451 p.Val344Leu missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85
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 1.0
rrs 1472207 n.362A>T non_coding_transcript_exon_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.88
PPE35 2169879 p.Phe245Cys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065958 c.234G>A synonymous_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 0.66
ald 3086742 c.-78A>C upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87
rpoA 3877956 p.Glu184Asp missense_variant 0.28
rpoA 3878641 c.-134C>G upstream_gene_variant 0.3
ddn 3987092 p.Glu83Asp missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.14
embA 4243346 c.114A>G synonymous_variant 0.58
embA 4243460 c.228C>T synonymous_variant 0.86
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247024 p.Pro171Ala missense_variant 0.26
embB 4248329 p.Met606Leu missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.79
ethA 4327062 p.Ser138Arg missense_variant 0.25
ethA 4327065 p.Cys137Arg missense_variant 0.54
whiB6 4338371 p.Thr51Pro missense_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 0.84