TB-Profiler result

Run: SRR18715359
Summary

Run ID: SRR18715359

Sample name:

Date: 03-04-2023 20:30:25

Number of reads: 2653883

Percentage reads mapped: 99.65

Strain: lineage4.8;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 0.14
lineage4 Euro-American LAM;T;S;X;H None 0.87
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.14
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.82
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.12
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 0.31 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.12 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid
pncA 2288792 c.449dupG frameshift_variant 0.19 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.16 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.24 ethionamide, 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 9304 p.Gly668Asp missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 0.16
mshA 576442 p.Cys365Trp missense_variant 0.19
mshA 576618 p.His424Pro missense_variant 0.43
ccsA 620625 p.Ile245Met missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 764367 p.Gly333Ala missense_variant 0.19
rpoC 764724 p.Phe452Cys missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.15
mmpL5 777883 p.Gly200Arg missense_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.78
fabG1 1673553 p.Asp38Glu missense_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 0.8
PPE35 2170065 p.Ala183Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.27
pepQ 2860159 p.Ala87Gly missense_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fbiD 3339751 p.Ala212Pro missense_variant 0.3
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.12
whiB7 3568420 p.Arg87Pro missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19
rpoA 3878580 c.-73A>C upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.55
embC 4240409 p.Pro183Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.22
embB 4246527 p.Ala5Gly missense_variant 0.37
embB 4246529 p.Ser6Gly missense_variant 0.17
embB 4247395 c.882C>T synonymous_variant 0.76
embB 4248328 c.1815G>C synonymous_variant 0.18
whiB6 4338200 p.Asp108His missense_variant 0.19
whiB6 4338371 p.Thr51Pro missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 0.15
gid 4408087 c.115dupC frameshift_variant 0.88