TB-Profiler result

Run: ERR5865193
Summary

Run ID: ERR5865193

Sample name:

Date: 01-04-2023 23:51:27

Number of reads: 763197

Percentage reads mapped: 13.31

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620477 p.Phe196Tyr missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759959 c.153G>A synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763851 p.Ala161Val missense_variant 0.11
rpoC 766383 p.Glu1005Gly missense_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 777457 p.Gly342Arg missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781925 c.366G>A synonymous_variant 0.2
fbiC 1302952 p.Lys8Glu missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473933 n.276C>A non_coding_transcript_exon_variant 0.12
rrl 1475346 n.1689C>T non_coding_transcript_exon_variant 0.14
rrl 1476561 n.2904C>T non_coding_transcript_exon_variant 0.15
inhA 1674426 c.225C>A synonymous_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155845 c.267G>A synonymous_variant 0.22
katG 2156115 c.-4T>C upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222991 c.174G>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288681 c.561A>G stop_lost&splice_region_variant 1.0
ahpC 2726527 p.Ser112Tyr missense_variant 0.11
folC 2746808 p.Ala264Glu missense_variant 0.25
ribD 2986921 c.88delC frameshift_variant 0.12
ald 3086693 c.-127G>T upstream_gene_variant 0.17
ald 3086703 c.-117T>G upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 0.95
fbiD 3339134 p.Asp6Gly missense_variant 0.14
fbiD 3339308 p.Pro64Leu missense_variant 0.2
fbiD 3339695 p.Ala193Asp missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641578 p.Leu15Pro missense_variant 0.25
alr 3841013 c.408C>T synonymous_variant 0.11
rpoA 3878240 p.Asp90Tyr missense_variant 0.15
rpoA 3878504 p.Leu2Met missense_variant 0.1
clpC1 4040873 c.-169T>A upstream_gene_variant 0.14
embC 4239753 c.-110C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244567 c.1335C>T synonymous_variant 0.15
embB 4246028 c.-486G>C upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268614 p.Gly75Trp missense_variant 0.22
ethA 4326308 p.Ala389Val missense_variant 0.11
ethA 4327307 p.Asp56Ala missense_variant 1.0
ethA 4327614 c.-141G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407581 p.Gly208Arg missense_variant 0.11
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0