TB-Profiler result

Run: SRR14807527
Summary

Run ID: SRR14807527

Sample name:

Date: 03-04-2023 12:26:35

Number of reads: 2004525

Percentage reads mapped: 99.56

Strain: lineage4.2.1;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 0.32
lineage4 Euro-American LAM;T;S;X;H None 0.63
lineage4.2 Euro-American H;T;LAM None 0.65
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.33
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.67
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 1.0 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.33 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.61 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.29 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.61 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.62 kanamycin
eis 2715369 c.-37G>T upstream_gene_variant 0.4 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.64 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.31 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.5 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
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 491247 c.465C>T synonymous_variant 0.65
fgd1 491742 c.960T>C synonymous_variant 0.35
mshA 575907 p.Ala187Val missense_variant 0.43
mshA 576108 p.Ala254Gly missense_variant 0.19
ccsA 619969 p.Val27Ile missense_variant 0.61
ccsA 620625 p.Ile245Met missense_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 0.18
rpoC 764817 p.Val483Gly missense_variant 0.72
rpoC 766645 p.Glu1092Asp missense_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
mmpL5 776182 p.Asp767Asn missense_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 0.45
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 0.36
PPE35 2169879 p.Phe245Cys missense_variant 0.77
PPE35 2170065 p.Ala183Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.31
pepQ 2860159 p.Ala87Gly missense_variant 0.19
ald 3086742 c.-78A>C upstream_gene_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.29
Rv3083 3449732 p.Leu410Pro missense_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32
rpoA 3878637 c.-130G>C upstream_gene_variant 0.12
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4249594 c.3081G>A synonymous_variant 0.62
aftB 4267647 p.Asp397Gly missense_variant 0.31
ethA 4326632 p.His281Pro missense_variant 0.7
ethA 4328376 c.-903G>C upstream_gene_variant 0.56
whiB6 4338563 c.-42G>T upstream_gene_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.46
gid 4407927 p.Glu92Asp missense_variant 0.36