TB-Profiler result

Run: ERR4813672
Summary

Run ID: ERR4813672

Sample name:

Date: 01-04-2023 12:55:12

Number of reads: 5905347

Percentage reads mapped: 99.69

Strain: lineage4.4.1.1;lineage4.3.3;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 0.65
lineage4 Euro-American LAM;T;S;X;H None 0.36
lineage4.3 Euro-American (LAM) mainly-LAM None 0.13
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.67
lineage4.4 Euro-American S;T None 0.23
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.68
lineage4.4.1 Euro-American (S-type) S;T None 0.22
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.13
lineage4.4.1.1 Euro-American S;Orphans None 0.23
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 0.14 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.64 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.19 isoniazid, ethionamide
katG 2155831 p.Asp94Gly missense_variant 0.61 isoniazid
ahpC 2726112 c.-81C>T upstream_gene_variant 0.47 isoniazid
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 8116 p.Thr272Ile missense_variant 0.27
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.64
mshA 575907 p.Ala187Val missense_variant 0.63
ccsA 620625 p.Ile245Met missense_variant 0.63
rpoB 761032 p.Gln409Arg missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.69
rpoC 764995 c.1626C>G synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.63
mmpL5 776182 p.Asp767Asn missense_variant 0.65
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
mmpS5 779630 c.-725T>C upstream_gene_variant 0.64
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.56
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.57
rpsA 1834683 p.Ala381Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 0.69
PPE35 2167926 p.Leu896Ser missense_variant 0.65
PPE35 2169840 p.Gly258Asp missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.12
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.72
thyA 3073868 p.Thr202Ala missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087755 c.936G>T synonymous_variant 0.74
Rv3083 3448608 c.105G>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73
clpC1 4038287 c.2418C>T synonymous_variant 0.11
embC 4242182 p.Ala774Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.6
embB 4247028 p.Leu172Arg missense_variant 0.26
aftB 4267647 p.Asp397Gly missense_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.65
gid 4407927 p.Glu92Asp missense_variant 0.62
gid 4408156 p.Leu16Arg missense_variant 0.14