TB-Profiler result

Run: ERR10748563
Summary

Run ID: ERR10748563

Sample name:

Date: 31-03-2023 10:58:55

Number of reads: 2811422

Percentage reads mapped: 99.26

Strain: lineage4.3.2.1;lineage4.1.1.3;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 0.54
lineage4 Euro-American LAM;T;S;X;H None 0.47
lineage4.3 Euro-American (LAM) mainly-LAM None 0.17
lineage4.1 Euro-American T;X;H None 0.26
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.56
lineage4.3.2 Euro-American (LAM) LAM3 None 0.18
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.51
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.26
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.26
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.16
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 0.72 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.5 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.44 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.5 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid
pncA 2289220 p.Asp8Asn missense_variant 0.46 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 0.44 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 0.16
gyrA 7222 c.-80C>T upstream_gene_variant 0.28
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 0.6
mshA 575907 p.Ala187Val missense_variant 0.6
mshA 576108 p.Ala254Gly missense_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 0.46
rpoC 763031 c.-339T>C upstream_gene_variant 0.55
rpoC 763555 c.186C>T synonymous_variant 0.56
rpoC 764995 c.1626C>G synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.46
mmpL5 776182 p.Asp767Asn missense_variant 0.55
mmpS5 778979 c.-74G>T upstream_gene_variant 0.61
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 0.27
Rv1258c 1406760 c.580_581insC frameshift_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.3
rpsA 1834177 c.636A>C synonymous_variant 0.47
tlyA 1917818 c.-122C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.54
PPE35 2167926 p.Leu896Ser missense_variant 0.65
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288856 p.Asp129Ala missense_variant 0.17
pepQ 2860159 p.Ala87Gly missense_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63
rpoA 3877956 p.Glu184Asp missense_variant 0.23
rpoA 3878590 c.-83G>C upstream_gene_variant 0.11
rpoA 3878608 c.-101C>G upstream_gene_variant 0.15
rpoA 3878641 c.-134C>G upstream_gene_variant 0.26
clpC1 4038287 c.2418C>T synonymous_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.3
embA 4243460 c.228C>T synonymous_variant 0.46
embB 4248324 p.Ala604Gly missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.53
gid 4407798 c.405G>T synonymous_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 0.6
gid 4407973 p.Val77Ala missense_variant 0.14
gid 4408150 p.Leu18Pro missense_variant 0.27
gid 4408156 p.Leu16Arg missense_variant 0.16