TB-Profiler result

Run: ERR133972
Summary

Run ID: ERR133972

Sample name:

Date: 31-03-2023 13:48:57

Number of reads: 9717674

Percentage reads mapped: 99.62

Strain: lineage4.8;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 0.51
lineage4 Euro-American LAM;T;S;X;H None 0.53
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.5
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.51
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.5
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 0.99 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.52 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.49 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.5 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 0.49 kanamycin
eis 2715369 c.-37G>T upstream_gene_variant 0.51 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.5 ethambutol
ethA 4326718 c.754_755dupGC frameshift_variant 0.45 ethionamide, ethionamide
ethA 4327480 c.-7T>C upstream_gene_variant 0.51 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 6432 p.Ala398Val missense_variant 0.47
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 0.52
fgd1 490751 c.-32T>G upstream_gene_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 0.55
mshA 575907 p.Ala187Val missense_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 0.55
rpoC 763031 c.-339T>C upstream_gene_variant 0.57
rpoC 764916 p.Leu516Pro missense_variant 0.48
rpoC 766645 p.Glu1092Asp missense_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776182 p.Asp767Asn missense_variant 0.51
mmpS5 779615 c.-710C>G upstream_gene_variant 0.46
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54
rpsA 1834177 c.636A>C synonymous_variant 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.49
PPE35 2167926 p.Leu896Ser missense_variant 0.55
PPE35 2168149 p.Pro822Ser missense_variant 0.53
PPE35 2169866 c.747G>C synonymous_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.55
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.52
Rv3083 3448383 c.-121T>C upstream_gene_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.53
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43
fbiB 3642793 p.Pro420Leu missense_variant 0.47
clpC1 4038857 c.1848C>A synonymous_variant 0.21
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 0.48
aftB 4267647 p.Asp397Gly missense_variant 0.43
whiB6 4338563 c.-42G>T upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.52
gid 4407927 p.Glu92Asp missense_variant 0.5