TB-Profiler result

Run: SRR10315458
Summary

Run ID: SRR10315458

Sample name:

Date: 02-04-2023 17:06:03

Number of reads: 6127289

Percentage reads mapped: 99.64

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 0.76
lineage4 Euro-American LAM;T;S;X;H None 0.21
lineage4.3 Euro-American (LAM) mainly-LAM None 0.22
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.79
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.22
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 761095 p.Leu430Pro missense_variant 0.81 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.19 rifampicin
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 0.23 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 0.12 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.18 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.19 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.27 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 8040 p.Gly247Ser missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491556 c.774G>A synonymous_variant 0.82
fgd1 491742 c.960T>C synonymous_variant 0.86
mshA 575907 p.Ala187Val missense_variant 0.74
mshA 576108 p.Ala254Gly missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.74
rpoB 761547 p.Val581Met missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.81
rpoC 764995 c.1626C>G synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.68
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.22
inhA 1674210 c.9A>C synonymous_variant 0.81
rpsA 1834177 c.636A>C synonymous_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.84
Rv1979c 2223051 p.Glu38Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.21
Rv2752c 3064519 c.1672delG frameshift_variant 0.75
Rv2752c 3065824 p.Pro123Leu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.78
clpC1 4038169 p.Ala846Pro missense_variant 0.82
clpC1 4038287 c.2418C>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.77
aftB 4267647 p.Asp397Gly missense_variant 0.76
whiB6 4338286 p.Val79Ala missense_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.19