TB-Profiler result

Run: SRR11972165
Summary

Run ID: SRR11972165

Sample name:

Date: 03-04-2023 05:30:18

Number of reads: 518981

Percentage reads mapped: 99.07

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 0.99
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 0.97
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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6590 p.Arg451Ser missense_variant 0.14
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 9531 p.Gly744Ser missense_variant 0.22
gyrA 9791 c.2490C>T synonymous_variant 0.33
fgd1 491152 p.Glu124Gln missense_variant 0.15
fgd1 491158 p.Lys126Glu missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760601 p.Asp265Glu missense_variant 0.4
rpoB 761082 p.Gly426Cys missense_variant 0.29
rpoB 762726 p.Ala974Thr missense_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.33
mmpL5 776021 c.2460G>C synonymous_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776430 p.Arg684Pro missense_variant 0.13
mmpL5 777191 c.1290C>A synonymous_variant 0.2
mmpL5 777196 p.Glu429Gln missense_variant 0.22
mmpL5 778101 p.Gln127Arg missense_variant 0.29
mmpL5 778489 c.-9G>A upstream_gene_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302821 c.-110G>A upstream_gene_variant 0.17
fbiC 1303151 p.Gly74Asp missense_variant 0.29
fbiC 1303273 p.Arg115Ser missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416480 p.Ala290Ser missense_variant 0.17
embR 1417526 c.-179G>T upstream_gene_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.26
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.17
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.22
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.22
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.22
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.25
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.2
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.2
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.21
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.12
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.12
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.23
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.22
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834264 c.723G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102668 c.375T>C synonymous_variant 0.17
ndh 2102671 c.372T>C synonymous_variant 0.17
ndh 2102875 c.168C>T synonymous_variant 0.12
ndh 2102912 p.Ala44Val missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154977 p.Ala379Thr missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.33
PPE35 2167967 c.2646A>C synonymous_variant 0.36
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2169974 c.639T>C synonymous_variant 0.17
PPE35 2170147 p.Ser156Ala missense_variant 0.15
PPE35 2170159 p.Ala152Ser missense_variant 0.2
PPE35 2170392 p.Gly74Ala missense_variant 0.22
PPE35 2170400 c.213G>C synonymous_variant 0.18
PPE35 2170403 c.210C>A synonymous_variant 0.18
PPE35 2170406 c.207A>G synonymous_variant 0.26
Rv1979c 2222145 p.Leu340Phe missense_variant 0.17
Rv1979c 2222200 p.Gly322Asp missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289733 c.-492G>A upstream_gene_variant 0.33
pncA 2289855 c.-614G>A upstream_gene_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.33
kasA 2518456 c.342C>T synonymous_variant 0.25
kasA 2518879 c.765A>G synonymous_variant 0.2
kasA 2518882 c.768C>A synonymous_variant 0.2
kasA 2519128 c.1014G>C synonymous_variant 0.29
kasA 2519131 c.1017G>C synonymous_variant 0.29
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715364 c.-32C>A upstream_gene_variant 0.4
ahpC 2726341 p.Val50Gly missense_variant 0.25
ribD 2986657 c.-182C>T upstream_gene_variant 0.25
thyA 3073696 p.Ala259Asp missense_variant 0.14
thyA 3073777 p.Leu232Pro missense_variant 0.14
thyA 3074580 c.-109T>C upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475102 p.Gly366Arg missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640757 p.Gly72Val missense_variant 0.15
fbiB 3642787 p.Trp418Leu missense_variant 0.33
alr 3840414 p.Pro336His missense_variant 0.4
alr 3840603 p.Pro273Leu missense_variant 0.18
rpoA 3877812 c.696C>A synonymous_variant 1.0
clpC1 4039161 p.His515Gly missense_variant 0.12
clpC1 4039372 p.Glu445* stop_gained 0.4
clpC1 4039594 p.Arg371Gly missense_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039754 c.951G>A synonymous_variant 0.17
clpC1 4039829 p.Leu292Ile missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246567 c.54_55insT frameshift_variant 0.4
embB 4248115 c.1602C>T synonymous_variant 0.82
embB 4249348 c.2835G>A synonymous_variant 0.4
aftB 4267606 p.Arg411Ser missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267881 p.Gly319Val missense_variant 0.4
aftB 4268279 c.556_557delCG frameshift_variant 0.15
ubiA 4269295 p.Met180Thr missense_variant 0.5
ethA 4326557 p.Arg306Leu missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethA 4327092 p.Ala128Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407643 p.Arg187Lys missense_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 1.0