TB-Profiler result

Run: ERR5865194
Summary

Run ID: ERR5865194

Sample name:

Date: 01-04-2023 23:51:28

Number of reads: 755060

Percentage reads mapped: 13.94

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 0.96 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
gyrB 5517 c.279delA frameshift_variant 0.11
gyrB 6779 c.1545_1547delCGA disruptive_inframe_deletion 0.11
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 575623 c.276C>T synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761600 c.1794T>C synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763112 p.Lys1102Asn missense_variant 0.13
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 777560 c.921C>A synonymous_variant 0.14
mmpL5 777612 p.Gly290Glu missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303978 p.Gly350Trp missense_variant 0.18
fbiC 1304559 p.Glu543Asp missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406955 p.Pro129Arg missense_variant 0.1
embR 1416895 p.Asp151Glu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473376 n.1531C>A non_coding_transcript_exon_variant 0.13
rpsA 1833470 c.-72T>C upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918654 p.Tyr239His missense_variant 0.12
ndh 2101918 c.1125G>A synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155472 p.Arg214Trp missense_variant 0.14
katG 2155664 p.Pro150Ala missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168693 c.1920T>C synonymous_variant 0.11
PPE35 2169088 p.Pro509Thr missense_variant 0.12
Rv1979c 2222157 c.1008G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288681 c.561A>G stop_lost&splice_region_variant 1.0
kasA 2518890 p.Ala259Asp missense_variant 0.11
Rv2752c 3065900 p.Pro98Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087067 p.Gly83Val missense_variant 0.11
fbiD 3339609 c.492G>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640593 c.55delG frameshift_variant 0.25
embC 4240211 p.Val117Ile missense_variant 0.18
embC 4241611 c.1749G>A synonymous_variant 0.13
embC 4242338 p.Thr826Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242701 p.Ala947Ser missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244322 p.Ala364Pro missense_variant 0.17
embA 4245054 p.Thr608Ser missense_variant 0.12
embB 4246028 c.-486G>C upstream_gene_variant 1.0
embB 4249613 p.Gly1034Ser missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268611 c.225delG frameshift_variant 0.33
ethA 4327307 p.Asp56Ala 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