TB-Profiler result

Run: SRR14782725
Summary

Run ID: SRR14782725

Sample name:

Date: 03-04-2023 11:36:32

Number of reads: 4309723

Percentage reads mapped: 99.52

Strain: lineage4.2.1;lineage4.1.2.1

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 1.0
lineage4.1 Euro-American T;X;H None 0.77
lineage4.2 Euro-American H;T;LAM None 0.23
lineage4.1.2 Euro-American T;H None 0.79
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.21
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.78
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 0.31 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.17 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.26 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.25 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.19 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
gyrA 9647 c.2346C>G synonymous_variant 0.18
fgd1 491247 c.465C>T synonymous_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 0.83
mshA 575679 p.Asn111Ser missense_variant 0.8
mshA 576108 p.Ala254Gly missense_variant 0.14
mshA 576113 p.Arg256Gly missense_variant 0.21
mshA 576613 c.1266A>C synonymous_variant 0.31
mshA 576616 c.1269G>C synonymous_variant 0.18
ccsA 619969 p.Val27Ile missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.79
rpoC 764537 p.Pro390Ala missense_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.13
PPE35 2170065 p.Ala183Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.82
kasA 2519071 p.Asp319Glu missense_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.18
ald 3086742 c.-78A>C upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.88
fbiD 3339746 p.Ala210Gly missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.21
whiB7 3568431 c.249C>G synonymous_variant 0.16
rpoA 3878597 c.-90G>C upstream_gene_variant 0.38
rpoA 3878608 c.-101C>G upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.65
clpC1 4039606 p.Glu367Gln missense_variant 0.83
embC 4240409 p.Pro183Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.81
embA 4243813 p.Arg194Gln missense_variant 0.79
embB 4246527 p.Ala5Gly missense_variant 0.29
embB 4248328 c.1815G>C synonymous_variant 0.17
embB 4249594 c.3081G>A synonymous_variant 0.16
ethA 4326632 p.His281Pro missense_variant 0.22
ethA 4328376 c.-903G>C upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0