TB-Profiler result

Run: ERR5865354

Summary

Run ID: ERR5865354

Sample name:

Date: 01-04-2023 23:58:01

Number of reads: 972553

Percentage reads mapped: 99.53

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 0.99
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 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7811 p.Phe170Leu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490714 c.-69G>T upstream_gene_variant 0.19
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575861 p.Pro172Thr missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619933 p.Asp15Tyr missense_variant 0.25
ccsA 620307 c.417C>A synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765461 p.Asn698His missense_variant 1.0
rpoC 765479 p.Tyr704His missense_variant 0.12
rpoC 766653 p.Ser1095Tyr missense_variant 0.4
rpoC 766709 p.Gly1114Cys missense_variant 0.29
rpoC 766889 p.Glu1174* stop_gained 0.17
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 776637 p.Glu615Gly missense_variant 0.12
mmpL5 777232 p.Asp417Tyr missense_variant 0.2
mmpL5 777571 p.Gly304Cys missense_variant 0.18
mmpL5 777935 c.546C>A synonymous_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303014 c.84G>T synonymous_variant 0.17
fbiC 1303705 p.Leu259Met missense_variant 0.17
Rv1258c 1406705 c.636C>A synonymous_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407481 c.-141G>T upstream_gene_variant 0.17
embR 1417109 p.Arg80Pro missense_variant 0.14
embR 1417222 p.Leu42Phe missense_variant 0.18
embR 1417387 c.-40C>A upstream_gene_variant 0.18
atpE 1460916 c.-129G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472403 n.558G>T non_coding_transcript_exon_variant 0.15
rrl 1473566 n.-92G>T upstream_gene_variant 0.2
rrl 1475619 n.1962C>A non_coding_transcript_exon_variant 0.2
rrl 1476289 n.2632C>A non_coding_transcript_exon_variant 0.15
fabG1 1673271 c.-169G>T upstream_gene_variant 0.15
rpsA 1833817 c.276C>A synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918743 c.804G>C synonymous_variant 0.22
ndh 2101785 p.Thr420Ala missense_variant 0.2
ndh 2101822 p.Phe407Leu missense_variant 0.18
ndh 2102231 p.Ser271* stop_gained 0.2
ndh 2102417 p.Ala209Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156300 c.-189G>T upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>A synonymous_variant 0.19
kasA 2518569 p.Ala152Glu missense_variant 0.2
eis 2715269 p.Ala22Ser missense_variant 0.14
folC 2746272 p.Ala443Ser missense_variant 0.17
pepQ 2860182 c.237C>A synonymous_variant 0.23
ribD 2987397 p.Leu187Met missense_variant 0.15
ribD 2987526 p.Gly230* stop_gained 0.15
Rv2752c 3065107 p.Val362Ala missense_variant 0.18
Rv2752c 3065110 p.Arg361Ile missense_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339692 p.Pro192His missense_variant 0.15
Rv3083 3449020 c.518delT frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474169 p.Pro55Thr missense_variant 0.17
fprA 3474228 c.222C>A synonymous_variant 0.18
Rv3236c 3612579 p.Glu180* stop_gained 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641873 c.339C>A synonymous_variant 0.21
fbiB 3641919 p.Ala129Ser missense_variant 0.18
alr 3840218 c.1203C>A synonymous_variant 0.25
rpoA 3878226 c.282C>A synonymous_variant 0.17
rpoA 3878518 c.-11G>T upstream_gene_variant 0.25
clpC1 4039516 p.Asp397His missense_variant 0.13
clpC1 4040222 p.Glu161Asp missense_variant 0.14
clpC1 4040693 c.12A>G synonymous_variant 0.12
embC 4240039 p.Leu59Phe missense_variant 0.18
embC 4240624 c.762C>A synonymous_variant 0.2
embC 4240637 p.His259Asn missense_variant 0.15
embC 4241945 c.2083C>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242691 c.-542C>A upstream_gene_variant 0.19
embA 4243160 c.-73C>A upstream_gene_variant 0.18
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244654 p.Gln474His missense_variant 0.17
embA 4244921 c.1689C>A synonymous_variant 0.22
embA 4245159 p.Ser643Gly missense_variant 0.17
embA 4245175 p.Ser648* stop_gained 0.23
embB 4249453 c.2940G>T synonymous_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268906 c.-70C>A upstream_gene_variant 0.18
whiB6 4338371 p.Thr51Pro missense_variant 1.0
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