TB-Profiler result

Run: SRR16088069
Summary

Run ID: SRR16088069

Sample name:

Date: 03-04-2023 16:03:45

Number of reads: 4320438

Percentage reads mapped: 99.64

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 0.33
lineage4 Euro-American LAM;T;S;X;H None 0.66
lineage4.3 Euro-American (LAM) mainly-LAM None 0.67
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.33
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.35
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.7
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 7570 p.Ala90Val missense_variant 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.12 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.24 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.69 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.33 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.85 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288841 p.Ala134Val missense_variant 0.29 pyrazinamide
pncA 2288850 c.391dupG frameshift_variant 0.31 pyrazinamide, pyrazinamide
pncA 2288883 p.Leu120Arg missense_variant 0.15 pyrazinamide
eis 2715339 c.-8delC upstream_gene_variant 0.21 kanamycin
eis 2715344 c.-12C>T upstream_gene_variant 0.76 kanamycin
folC 2747480 p.Glu40Gly missense_variant 0.15 para-aminosalicylic_acid
embA 4243221 c.-12C>T upstream_gene_variant 0.23 ethambutol
embB 4247429 p.Met306Val missense_variant 0.15 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.23 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.75
gyrA 8205 p.Ile302Val missense_variant 0.41
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.35
mshA 575907 p.Ala187Val missense_variant 0.36
ccsA 620625 p.Ile245Met missense_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
rpoC 764367 p.Gly333Ala missense_variant 0.19
rpoC 764817 p.Val483Gly missense_variant 0.88
rpoC 764918 p.Val517Leu missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.59
rpoC 766645 p.Glu1092Asp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.28
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpL5 777883 p.Gly200Arg missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.58
fbiC 1304962 p.Trp678Gly missense_variant 0.55
Rv1258c 1406760 c.580_581insC frameshift_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.28
rpsA 1834177 c.636A>C synonymous_variant 0.34
rpsA 1834836 p.Met432Thr missense_variant 0.65
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.28
katG 2156196 c.-85C>T upstream_gene_variant 0.66
PPE35 2167926 p.Leu896Ser missense_variant 0.31
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288682 c.560G>C stop_lost&splice_region_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 0.62
kasA 2519071 p.Asp319Glu missense_variant 0.25
folC 2746340 p.Ala420Val missense_variant 0.72
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ribD 2986827 c.-12G>A upstream_gene_variant 0.63
thyA 3073868 p.Thr202Ala missense_variant 0.66
ald 3086731 c.-89A>G upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086791 c.-29T>C upstream_gene_variant 0.69
ald 3087532 p.Ala238Asp missense_variant 0.21
fbiD 3339734 p.Ala206Gly missense_variant 0.61
fbiD 3339746 p.Ala210Gly missense_variant 0.31
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.2
Rv3236c 3612229 c.888C>T synonymous_variant 0.21
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44
rpoA 3878637 c.-130G>C upstream_gene_variant 0.4
rpoA 3878641 c.-134C>G upstream_gene_variant 0.7
clpC1 4038287 c.2418C>T synonymous_variant 0.71
clpC1 4038968 c.1737G>A synonymous_variant 0.7
embC 4240409 p.Pro183Ala missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.22
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4248328 c.1815G>C synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.37
ethA 4326855 p.Arg207Cys missense_variant 0.14
whiB6 4338371 p.Thr51Pro missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.31
gid 4407927 p.Glu92Asp missense_variant 0.3
gid 4408156 p.Leu16Arg missense_variant 0.67