TB-Profiler result

Run: SRR23310868
Summary

Run ID: SRR23310868

Sample name:

Date: 14-03-2023 01:08:54

Number of reads: 2846415

Percentage reads mapped: 99.58

Strain: lineage4.2.1;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 0.36
lineage4.2 Euro-American H;T;LAM None 0.65
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.36
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.34
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.65
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
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.69 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.18 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.68 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.389_390insGG frameshift_variant 0.62 pyrazinamide, pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.66 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.39 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.44 para-aminosalicylic_acid
embB 4247402 p.Ser297Ala missense_variant 0.71 ethambutol
embB 4247429 p.Met306Val missense_variant 0.32 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 0.99
gyrA 7581 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.63
fgd1 491742 c.960T>C synonymous_variant 0.38
mshA 575907 p.Ala187Val missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576482 p.Val379Leu missense_variant 0.23
ccsA 619969 p.Val27Ile missense_variant 0.7
ccsA 620625 p.Ile245Met missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 0.4
rpoC 764817 p.Val483Gly missense_variant 0.67
rpoC 764916 p.Leu516Pro missense_variant 0.36
rpoC 766645 p.Glu1092Asp missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.32
mmpL5 776182 p.Asp767Asn missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.38
PPE35 2167926 p.Leu896Ser missense_variant 0.36
PPE35 2169879 p.Phe245Cys missense_variant 0.7
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.63
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.33
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
fbiB 3641810 c.276G>C synonymous_variant 0.41
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.36
embB 4246584 p.Arg24Pro missense_variant 0.33
embB 4248324 p.Ala604Gly missense_variant 0.19
embB 4249594 c.3081G>A synonymous_variant 0.61
aftB 4267647 p.Asp397Gly missense_variant 0.44
ethA 4326339 p.Asn379Asp missense_variant 0.28
ethA 4326632 p.His281Pro missense_variant 0.67
ethA 4328376 c.-903G>C upstream_gene_variant 0.58
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.45
gid 4407927 p.Glu92Asp missense_variant 0.37