TB-Profiler result

Run: SRR21747017
Summary

Run ID: SRR21747017

Sample name:

Date: 04-04-2023 03:27:46

Number of reads: 2266021

Percentage reads mapped: 99.66

Strain: lineage4.5;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 0.86
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.5 Euro-American H;T RD122 0.15
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.85
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.84
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 0.13 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
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 7892 c.591G>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.92
ccsA 620029 c.139C>T synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.73
rpoC 763031 c.-339T>C upstream_gene_variant 0.85
rpoC 764248 c.879C>G synonymous_variant 0.13
rpoC 764944 p.His525Gln missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.8
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406586 p.Thr252Asn missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81
Rv1258c 1406796 p.Gly182Val missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.87
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.83
PPE35 2167926 p.Leu896Ser missense_variant 0.85
PPE35 2170568 p.Ile15Met missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288754 p.Val163Ala missense_variant 0.1
thyA 3074582 c.-111T>G upstream_gene_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
rpoA 3878575 c.-68C>T upstream_gene_variant 0.12
clpC1 4038318 p.Pro796Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.85
embB 4247573 p.Asp354Asn missense_variant 0.21
aftB 4267647 p.Asp397Gly missense_variant 0.8
ethA 4326676 p.Ser266Arg missense_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.89
gid 4407927 p.Glu92Asp missense_variant 0.85