TB-Profiler result

Run: SRR1163147
Summary

Run ID: SRR1163147

Sample name:

Date: 02-04-2023 23:32:25

Number of reads: 1042714

Percentage reads mapped: 98.59

Strain: lineage4.1.2.1;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 0.22
lineage4.1 Euro-American T;X;H None 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.81
lineage4.1.2 Euro-American T;H None 0.12
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.8
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.17
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 0.86 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.63 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.69 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid
pncA 2289248 c.-7T>C upstream_gene_variant 0.65 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.79 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.79 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 491591 p.Lys270Met missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.76
mshA 575679 p.Asn111Ser missense_variant 0.18
mshA 575907 p.Ala187Val missense_variant 0.92
ccsA 620337 c.447C>A synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 0.7
rpoB 760115 c.309C>T synonymous_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 0.68
rpoC 764817 p.Val483Gly missense_variant 0.66
rpoC 765150 p.Gly594Glu missense_variant 0.24
rpoC 766645 p.Glu1092Asp missense_variant 0.8
rpoC 766824 p.Lys1152Arg missense_variant 0.13
rpoC 766833 p.Glu1155Gly missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.79
mmpL5 776182 p.Asp767Asn missense_variant 0.8
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78
embR 1416663 p.Arg229Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834103 p.Arg188Ser missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.83
tlyA 1917763 c.-177T>C upstream_gene_variant 0.14
tlyA 1917774 c.-166C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.75
katG 2155846 p.Pro89Gln missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.79
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.19
folC 2746833 p.Val256Met missense_variant 0.15
pepQ 2860440 c.-22G>A upstream_gene_variant 0.15
pepQ 2860482 c.-64A>T upstream_gene_variant 0.13
ribD 2987240 c.402C>T synonymous_variant 0.12
Rv2752c 3065725 p.Ile156Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 0.69
Rv3083 3448325 c.-179G>A upstream_gene_variant 0.12
Rv3083 3448336 c.-168G>C upstream_gene_variant 0.12
Rv3083 3448348 c.-156G>C upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 0.81
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77
clpC1 4038763 p.Thr648Ser missense_variant 0.12
embC 4242199 c.2337C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 0.81
embA 4243869 p.Ala213Pro missense_variant 0.11
embA 4244072 c.840C>T synonymous_variant 0.13
embB 4248493 p.Met660Ile missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.84
aftB 4269339 c.-503C>T upstream_gene_variant 0.77
ethR 4328128 p.Val194Met missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.88
gid 4407927 p.Glu92Asp missense_variant 0.89