TB-Profiler result

Run: ERR4827446
Summary

Run ID: ERR4827446

Sample name:

Date: 01-04-2023 18:03:36

Number of reads: 809561

Percentage reads mapped: 99.37

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
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
embB 4247730 p.Gly406Ala 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 5950 c.711A>G synonymous_variant 0.12
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 491010 c.228C>A synonymous_variant 0.15
fgd1 491169 p.Phe129Leu missense_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576358 c.1012delA frameshift_variant 0.11
mshA 576396 p.Ser350Asn missense_variant 0.12
mshA 576398 p.Tyr351Asp missense_variant 0.12
mshA 576403 c.1056C>G synonymous_variant 0.12
mshA 576459 c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG frameshift_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761338 c.1533delC frameshift_variant 0.13
rpoB 761456 p.Glu550Asp missense_variant 0.13
rpoB 762516 p.Gly904Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>C synonymous_variant 0.18
mmpL5 775952 c.2529G>C synonymous_variant 0.11
mmpL5 775955 p.Ile842Leu missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778842 p.Gly22Ser missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781588 p.Lys10Met missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.13
Rv1258c 1406946 p.Ala132Gly missense_variant 0.14
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102030 p.Gln338Arg missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223079 p.Gly29Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860162 p.Arg86Gln missense_variant 0.13
Rv2752c 3064891 p.Gly434Asp missense_variant 0.13
thyX 3067387 p.Gly187Ser missense_variant 0.13
thyA 3074423 p.Pro17Thr missense_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339364 p.Pro83Ala missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641981 c.447C>T synonymous_variant 0.13
rpoA 3877939 p.Asp190Gly missense_variant 1.0
embC 4242092 c.2230T>C synonymous_variant 0.12
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 4244746 p.Leu505His missense_variant 0.15
embA 4245834 c.2610_2612dupGGT disruptive_inframe_insertion 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 0.33
aftB 4268559 p.Leu93Pro missense_variant 0.17
ethA 4327253 p.Ala74Glu missense_variant 1.0
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 0.93