TB-Profiler result

Run: ERR2864261
Summary

Run ID: ERR2864261

Sample name:

Date: 31-03-2023 23:54:57

Number of reads: 414540

Percentage reads mapped: 99.57

Strain: 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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 1.0 para-aminosalicylic_acid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9759 p.Glu820Lys missense_variant 0.13
fgd1 490729 c.-54C>A upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575248 c.-100C>T upstream_gene_variant 0.29
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619717 c.-174G>A upstream_gene_variant 0.13
ccsA 620133 c.243G>C synonymous_variant 0.18
ccsA 620194 p.Thr102Ser missense_variant 0.17
ccsA 620364 c.474C>A synonymous_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767189 p.Pro1274Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777680 c.801G>C synonymous_variant 0.15
mmpR5 779233 p.Arg82Trp missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781924 p.Glu122Gly missense_variant 0.22
rplC 800674 c.-135A>G upstream_gene_variant 0.11
fbiC 1304626 p.Ala566Pro missense_variant 0.12
Rv1258c 1406749 p.Lys198Glu missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474045 n.388C>T non_coding_transcript_exon_variant 0.11
rrl 1474238 n.581G>A non_coding_transcript_exon_variant 0.13
rrl 1476342 n.2685G>T non_coding_transcript_exon_variant 1.0
inhA 1673730 c.-472C>T upstream_gene_variant 0.18
rpsA 1833430 c.-112T>C upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154077 p.Gln679* stop_gained 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155836 c.276C>A synonymous_variant 0.13
katG 2156325 c.-214C>T upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517975 c.-140A>T upstream_gene_variant 0.14
folC 2747091 p.Val170Met missense_variant 0.12
thyX 3067339 p.His203Tyr missense_variant 0.25
thyA 3073880 c.591delC frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087306 p.Val163Met missense_variant 0.18
ald 3087527 c.712dupG frameshift_variant 1.0
ald 3087562 p.Lys248Arg missense_variant 0.2
Rv3083 3448367 c.-137G>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475249 p.Pro415Ser missense_variant 0.2
whiB7 3568866 c.-187C>T upstream_gene_variant 0.14
Rv3236c 3612425 p.Ala231Glu missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641810 c.276G>C synonymous_variant 1.0
rpoA 3878132 p.Ala126Thr missense_variant 0.13
clpC1 4039603 p.Ala368Ser missense_variant 0.11
clpC1 4039950 p.Leu252Pro missense_variant 0.13
clpC1 4039955 c.750G>A synonymous_variant 0.12
clpC1 4040838 c.-134C>T upstream_gene_variant 0.11
embC 4241322 p.Ile487Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244597 c.1365G>T synonymous_variant 0.11
embA 4245213 p.Ala661Thr missense_variant 0.11
embB 4246451 c.-63T>A upstream_gene_variant 0.13
embB 4246980 p.Gly156Asp missense_variant 0.15
embB 4247198 p.Thr229Ser missense_variant 0.11
embB 4248027 p.Ala505Val missense_variant 1.0
aftB 4267224 p.Ile538Thr missense_variant 0.2
aftB 4267324 p.Ile505Phe missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326339 p.Asn379Asp missense_variant 1.0
ethA 4328387 c.-914A>T upstream_gene_variant 0.12
ethA 4328390 c.-917G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0