TB-Profiler result

Run: SRR18715461
Summary

Run ID: SRR18715461

Sample name:

Date: 03-04-2023 20:35:24

Number of reads: 3925307

Percentage reads mapped: 99.54

Strain: lineage4.3.3;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 0.89
lineage4 Euro-American LAM;T;S;X;H None 0.13
lineage4.3 Euro-American (LAM) mainly-LAM None 0.1
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.87
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.88
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.11
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
rpoC 764363 p.Gly332Arg missense_variant 0.69 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin
katG 2155109 p.Ile335Val missense_variant 0.85 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.12 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.89 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 491742 c.960T>C synonymous_variant 0.86
mshA 576108 p.Ala254Gly missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 763612 p.Glu81Asp missense_variant 0.69
rpoC 764995 c.1626C>G synonymous_variant 0.13
rpoC 766488 p.Pro1040Arg missense_variant 0.14
rpoC 766667 p.Ser1100Ala missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302917 c.-14_-13insA upstream_gene_variant 0.83
Rv1258c 1406760 c.580_581insC frameshift_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.88
rpsA 1834776 p.Ala412Val missense_variant 0.9
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.81
PPE35 2170065 p.Ala183Gly missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 0.13
fbiD 3339734 p.Ala206Gly missense_variant 0.57
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 0.91
fbiB 3640879 c.-656C>T upstream_gene_variant 0.85
alr 3840953 c.468C>T synonymous_variant 0.16
rpoA 3878613 c.-106A>C upstream_gene_variant 0.4
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.82
embA 4243598 c.366G>A synonymous_variant 0.87
embA 4244823 p.Val531Leu missense_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4247872 c.1359C>T synonymous_variant 0.87
embB 4248316 c.1803C>T synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.88
ethA 4326474 p.Pro334Ala missense_variant 0.88
whiB6 4338326 p.Ala66Thr missense_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.87
gid 4408009 p.Val65Ala missense_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.14