TB-Profiler result

Run: SRR7516374
Summary

Run ID: SRR7516374

Sample name:

Date: 04-04-2023 19:26:24

Number of reads: 2016102

Percentage reads mapped: 99.65

Strain: lineage4.3.3;lineage2.2.1

Drug-resistance: Pre-XDR-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 0.57
lineage4 Euro-American LAM;T;S;X;H None 0.42
lineage4.3 Euro-American (LAM) mainly-LAM None 0.42
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.58
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.42
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
gyrA 7582 p.Asp94Ala missense_variant 0.32 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.48 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.51 isoniazid, ethionamide
fabG1 1673425 c.-15C>T upstream_gene_variant 0.49 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.29 pyrazinamide
pncA 2289252 c.-11A>C upstream_gene_variant 0.5 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.41 kanamycin
embB 4247429 p.Met306Val missense_variant 0.38 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.5 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.51
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.73
mshA 575907 p.Ala187Val missense_variant 0.64
mshA 576108 p.Ala254Gly missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.47
rpoC 764918 p.Val517Leu missense_variant 0.39
rpoC 764995 c.1626C>G synonymous_variant 0.43
rpoC 766645 p.Glu1092Asp missense_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.65
mmpL5 776182 p.Asp767Asn missense_variant 0.55
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475932 n.2275T>C non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.48
rpsA 1834836 p.Met432Thr missense_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.51
katG 2156196 c.-85C>T upstream_gene_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.41
folC 2746340 p.Ala420Val missense_variant 0.47
thyA 3073868 p.Thr202Ala missense_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086941 c.125dupG frameshift_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 0.72
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 0.35
clpC1 4038968 c.1737G>A synonymous_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.58
aftB 4267647 p.Asp397Gly missense_variant 0.54
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.67
gid 4407857 p.Arg116Trp missense_variant 0.43
gid 4407927 p.Glu92Asp missense_variant 0.59
gid 4408156 p.Leu16Arg missense_variant 0.45