TB-Profiler result

Run: SRR6785155
Summary

Run ID: SRR6785155

Sample name:

Date: 04-04-2023 15:33:16

Number of reads: 2944100

Percentage reads mapped: 99.72

Strain: lineage4.3;lineage2.2.1

Drug-resistance: HR-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 0.58
lineage4.3 Euro-American (LAM) mainly-LAM None 0.36
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.53
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.55
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
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.3 para-aminosalicylic_acid
ethA 4327322 p.Pro51Leu missense_variant 0.44 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 0.98
gyrA 8040 p.Gly247Ser missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491315 p.Gly178Ala missense_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 0.71
mshA 575907 p.Ala187Val missense_variant 0.65
mshA 576108 p.Ala254Gly missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 0.54
rpoB 761799 p.Arg665Trp missense_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.6
rpoC 764995 c.1626C>G synonymous_variant 0.3
rpoC 766645 p.Glu1092Asp missense_variant 0.79
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.65
mmpL5 776182 p.Asp767Asn missense_variant 0.66
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304671 p.Val581Leu missense_variant 0.67
Rv1258c 1406760 c.580_581insC frameshift_variant 0.62
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.4
rrs 1472564 n.719A>G non_coding_transcript_exon_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 0.7
rpsA 1834836 p.Met432Thr missense_variant 0.36
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.62
PPE35 2167926 p.Leu896Ser missense_variant 0.5
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.35
Rv2752c 3067135 c.-944C>T upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 0.34
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 0.47
rpoA 3878490 c.18C>G synonymous_variant 0.5
clpC1 4038287 c.2418C>T synonymous_variant 0.55
panD 4043867 p.Gly139* stop_gained 0.49
embC 4241948 p.Phe696Leu missense_variant 0.45
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.72
aftB 4267647 p.Asp397Gly missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.72
gid 4407720 c.483C>G synonymous_variant 0.26
gid 4407913 p.Arg97His missense_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 0.67
gid 4408156 p.Leu16Arg missense_variant 0.43