TB-Profiler result

Run: SRR14807461
Summary

Run ID: SRR14807461

Sample name:

Date: 03-04-2023 12:24:01

Number of reads: 2722261

Percentage reads mapped: 99.53

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
lineage4 Euro-American LAM;T;S;X;H None 0.91
lineage4.2 Euro-American H;T;LAM None 0.9
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.09
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.91
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
rpsL 781822 p.Lys88Arg missense_variant 0.88 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.9 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.89 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.89 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.11 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 491247 c.465C>T synonymous_variant 0.92
fgd1 491742 c.960T>C synonymous_variant 0.1
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619969 p.Val27Ile missense_variant 0.91
rpoB 762286 p.Arg827Leu missense_variant 0.15
rpoC 764817 p.Val483Gly missense_variant 0.89
rpoC 766645 p.Glu1092Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086695 c.-125C>T upstream_gene_variant 0.13
ald 3086742 c.-78A>C upstream_gene_variant 0.85
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.32
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11
rpoA 3878641 c.-134C>G upstream_gene_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4249594 c.3081G>A synonymous_variant 0.95
aftB 4267647 p.Asp397Gly missense_variant 0.13
ethA 4326632 p.His281Pro missense_variant 0.94
ethA 4328376 c.-903G>C upstream_gene_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.15