TB-Profiler result

Run: SRR14782658
Summary

Run ID: SRR14782658

Sample name:

Date: 03-04-2023 11:34:28

Number of reads: 4690716

Percentage reads mapped: 99.46

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 0.28
lineage4 Euro-American LAM;T;S;X;H None 0.73
lineage4.2 Euro-American H;T;LAM None 0.73
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.28
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.77
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 781687 p.Lys43Arg missense_variant 0.25 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.78 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.73 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288887 p.Trp119Arg missense_variant 0.23 pyrazinamide
pncA 2289040 p.Trp68Arg missense_variant 0.71 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.72 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.69 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.26 ethambutol
ethA 4327033 p.Tyr147* stop_gained 0.3 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 0.83
fgd1 491742 c.960T>C synonymous_variant 0.28
mshA 575907 p.Ala187Val missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576613 c.1266A>C synonymous_variant 0.22
mshA 576616 c.1269G>C synonymous_variant 0.31
ccsA 619969 p.Val27Ile missense_variant 0.76
ccsA 620625 p.Ile245Met missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 764367 p.Gly333Ala missense_variant 0.15
rpoC 764817 p.Val483Gly missense_variant 0.7
rpoC 764840 p.Ile491Val missense_variant 0.26
rpoC 766645 p.Glu1092Asp missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.28
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpL5 777883 p.Gly200Arg missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.23
rpsA 1834177 c.636A>C synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 0.24
PPE35 2169879 p.Phe245Cys missense_variant 0.78
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.23
pepQ 2860159 p.Ala87Gly missense_variant 0.19
Rv2752c 3064823 p.Val457Leu missense_variant 0.16
ald 3086742 c.-78A>C upstream_gene_variant 0.71
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339734 p.Ala206Gly missense_variant 0.73
fbiD 3339746 p.Ala210Gly missense_variant 0.38
fbiD 3339749 p.Val211Gly missense_variant 0.38
fbiD 3339751 p.Ala212Pro missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.2
whiB7 3568428 c.252A>G synonymous_variant 0.35
whiB7 3568431 c.249C>G synonymous_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.14
fbiB 3640830 c.-705C>A upstream_gene_variant 0.79
rpoA 3878590 c.-83G>C upstream_gene_variant 0.3
rpoA 3878597 c.-90G>C upstream_gene_variant 0.2
rpoA 3878609 c.-102T>G upstream_gene_variant 0.22
rpoA 3878613 c.-106A>C upstream_gene_variant 0.38
rpoA 3878628 c.-121G>T upstream_gene_variant 0.4
rpoA 3878637 c.-130G>C upstream_gene_variant 0.67
rpoA 3878641 c.-134C>G upstream_gene_variant 0.77
embC 4240409 p.Pro183Ala missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>A upstream_gene_variant 0.26
embA 4243460 c.228C>T synonymous_variant 0.3
embB 4246527 p.Ala5Gly missense_variant 0.28
embB 4247020 c.507C>G synonymous_variant 0.21
embB 4248324 p.Ala604Gly missense_variant 0.18
embB 4248328 c.1815G>C synonymous_variant 0.26
embB 4249594 c.3081G>A synonymous_variant 0.72
aftB 4267647 p.Asp397Gly missense_variant 0.16
ethA 4326632 p.His281Pro missense_variant 0.77
ethA 4328376 c.-903G>C upstream_gene_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.26
gid 4407927 p.Glu92Asp missense_variant 0.29