TB-Profiler result

Run: SRR11972164
Summary

Run ID: SRR11972164

Sample name:

Date: 03-04-2023 05:30:39

Number of reads: 598500

Percentage reads mapped: 99.14

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.98
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288697 p.Leu182Ser missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.5 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
gyrA 9564 p.Tyr755Asn missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575746 c.399C>T synonymous_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762248 c.2442G>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765822 p.Ala818Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775864 p.Ala873Ser missense_variant 0.15
mmpL5 775865 c.2616T>G synonymous_variant 0.15
mmpL5 775927 c.2554C>T synonymous_variant 0.2
mmpL5 775931 c.2550C>T synonymous_variant 0.25
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778956 c.-476G>C upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303005 c.75G>T synonymous_variant 0.22
fbiC 1303016 p.Val29Gly missense_variant 0.27
fbiC 1303107 c.177C>T synonymous_variant 0.29
fbiC 1304293 p.Thr455Ala missense_variant 0.29
fbiC 1305316 c.2389delC frameshift_variant 0.15
Rv1258c 1406299 p.Val348Ile missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>T non_coding_transcript_exon_variant 0.31
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.66
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.68
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.6
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.52
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.48
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.15
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.16
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.17
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.15
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.15
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.28
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.28
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.28
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.29
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.29
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.29
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.17
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
fabG1 1674085 p.Glu216Lys missense_variant 0.29
rpsA 1833558 p.Val6Asp missense_variant 0.14
rpsA 1833565 c.24G>C synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834292 c.752delT frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102392 c.650_651insA frameshift_variant 0.22
ndh 2102968 c.75C>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167898 c.2715G>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.38
PPE35 2170171 p.Val148Ile missense_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.17
Rv1979c 2222949 c.216C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289705 c.-464G>T upstream_gene_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.33
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
ahpC 2726350 p.Trp53Leu missense_variant 0.2
ahpC 2726456 c.264C>T synonymous_variant 0.17
thyA 3074653 c.-182G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448402 c.-102C>T upstream_gene_variant 0.25
Rv3083 3448641 c.138C>T synonymous_variant 0.18
Rv3083 3448650 c.147C>T synonymous_variant 0.18
Rv3083 3448653 c.150C>T synonymous_variant 0.18
Rv3083 3448656 c.153G>C synonymous_variant 0.18
Rv3083 3448660 p.Val53Ile missense_variant 0.18
Rv3083 3448665 c.162T>C synonymous_variant 0.22
Rv3083 3448668 c.165G>C synonymous_variant 0.22
Rv3083 3448859 p.Ala119Glu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.25
fprA 3474708 c.702C>T synonymous_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841203 p.Gly73Val missense_variant 0.22
ddn 3987019 p.Pro59Leu missense_variant 0.33
ddn 3987060 p.Val73Ile missense_variant 0.29
clpC1 4039645 p.His354Asp missense_variant 0.24
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4039829 p.Leu292Ile missense_variant 0.18
embC 4239854 c.-9G>T upstream_gene_variant 0.2
embC 4240655 p.Ala265Pro missense_variant 0.4
embC 4240801 c.939C>T synonymous_variant 0.38
embC 4240803 p.Tyr314Phe missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245330 p.Gly700Ser missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4247426 p.Gly305Thr missense_variant 0.4
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248500 p.Ile663Val missense_variant 0.15
embB 4248803 p.Met764Val missense_variant 0.33
embB 4248977 p.Thr822Ala missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268622 p.Trp72* stop_gained 0.25
ubiA 4269265 p.Gly190Asp missense_variant 0.22
aftB 4269702 c.-866C>A upstream_gene_variant 0.25
ubiA 4269791 p.Ala15Thr missense_variant 0.29
ubiA 4269794 p.Val14Phe missense_variant 0.29
ethA 4328366 c.-893G>A upstream_gene_variant 0.18
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
gid 4408124 p.Ala27Ser missense_variant 0.25