TB-Profiler result

Run: ERR8665802
Summary

Run ID: ERR8665802

Sample name:

Date: 02-04-2023 07:40:07

Number of reads: 449904

Percentage reads mapped: 19.31

Strain: 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 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.95 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288727 p.Leu172Pro missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA 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 6304 c.-998C>G upstream_gene_variant 0.18
gyrA 6454 c.-848C>A upstream_gene_variant 0.22
gyrB 7227 p.Ile663Thr missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Cys missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8538 p.Thr413Ala missense_variant 0.17
gyrA 9066 c.1765C>A synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9459 p.Gly720Cys missense_variant 0.22
fgd1 490694 c.-89G>T upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491788 p.Gly336Ser missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759825 p.Ser7Gly missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765614 p.Tyr749His missense_variant 0.4
rpoC 765751 c.2382C>A synonymous_variant 0.33
rpoC 766355 p.Gly996Cys missense_variant 0.15
rpoC 766363 c.2994G>T synonymous_variant 0.17
rpoC 766498 p.Lys1043Asn missense_variant 0.12
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 777810 p.Arg224Leu missense_variant 0.29
mmpL5 777836 c.645C>A synonymous_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781802 c.243G>T synonymous_variant 0.12
rplC 801419 p.Gly204Val missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406834 c.507C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472311 n.466C>A non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.32
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.48
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.69
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.93
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.93
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.92
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.93
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.69
rrs 1472827 n.982G>A non_coding_transcript_exon_variant 0.35
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.35
rrs 1473324 n.1479G>T non_coding_transcript_exon_variant 0.13
rrl 1475421 n.1764C>A non_coding_transcript_exon_variant 0.12
rrl 1476017 n.2360G>T non_coding_transcript_exon_variant 0.12
rrl 1476370 n.2713C>A non_coding_transcript_exon_variant 0.12
inhA 1673613 c.-589C>A upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102473 c.570C>A synonymous_variant 0.17
ndh 2102852 p.Ser64Tyr missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221759 p.Arg469Leu missense_variant 0.13
Rv1979c 2223284 c.-120C>A upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289465 c.-224G>T upstream_gene_variant 0.14
pncA 2289490 c.-249C>A upstream_gene_variant 0.2
folC 2746629 p.Asp324Asn missense_variant 0.29
folC 2746948 c.651G>T synonymous_variant 0.25
folC 2746959 p.Gly214Trp missense_variant 0.22
folC 2747272 c.327G>T synonymous_variant 0.2
ribD 2987613 c.775T>C stop_lost&splice_region_variant 0.17
thyX 3067656 p.Arg97Leu missense_variant 0.33
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449454 c.951G>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475362 c.1356G>T synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612880 c.237G>T synonymous_variant 0.2
fbiA 3640828 p.Gly96Cys missense_variant 0.2
fbiA 3641202 c.662delG frameshift_variant 0.5
fbiB 3642363 p.Glu277* stop_gained 0.22
alr 3840989 c.432G>T synonymous_variant 0.22
alr 3841169 c.252C>A synonymous_variant 0.2
alr 3841183 p.Thr80Pro missense_variant 0.18
ddn 3986996 c.153C>A synonymous_variant 0.25
embC 4241319 p.Pro486Gln missense_variant 0.29
embC 4241815 c.1953G>T synonymous_variant 0.2
embA 4242475 c.-758G>A upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243857 p.Leu209Ile missense_variant 0.25
embB 4245542 c.-972C>T upstream_gene_variant 0.29
embB 4245629 c.-885C>A upstream_gene_variant 0.17
embB 4246669 c.156C>T synonymous_variant 0.33
embB 4247226 p.Arg238His missense_variant 0.17
embB 4249797 p.Arg1095Leu missense_variant 0.15
aftB 4267164 p.Trp558Leu missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268623 p.Trp72Arg missense_variant 0.2
ubiA 4269230 p.Thr202Ala missense_variant 0.17
ethA 4326340 c.1134C>T synonymous_variant 0.15
ethR 4327021 c.-528G>A upstream_gene_variant 0.15
ethA 4327031 p.Ser148* stop_gained 0.15
ethR 4327864 p.Gly106Trp missense_variant 0.22
ethA 4328276 c.-803C>T upstream_gene_variant 0.17
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 4407624 c.579G>T synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0