TB-Profiler result

Run: SRR6257088
Summary

Run ID: SRR6257088

Sample name:

Date: 04-04-2023 13:25:54

Number of reads: 643813

Percentage reads mapped: 100.0

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 0.88 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747480 p.Glu40Gly missense_variant 1.0 para-aminosalicylic_acid
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 575815 p.Trp156Cys missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619807 c.-84G>T upstream_gene_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.3
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763870 p.Asp167Glu missense_variant 0.18
rpoC 764918 p.Val517Leu missense_variant 0.94
rpoC 765265 p.Lys632Asn missense_variant 0.14
rpoC 766635 p.Phe1089Ser missense_variant 0.12
rpoC 766874 p.Asp1169Tyr missense_variant 0.12
rpoC 767065 c.3696G>T synonymous_variant 0.11
rpoC 767293 p.Asp1308Glu missense_variant 0.13
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 777451 p.Val344Leu missense_variant 0.12
mmpL5 777740 c.741G>A synonymous_variant 0.2
mmpL5 777880 p.Asp201Tyr 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 1303016 p.Val29Gly missense_variant 0.25
fbiC 1303480 p.Gln184Lys missense_variant 0.12
fbiC 1304275 p.Leu449Met missense_variant 0.12
fbiC 1304282 p.Ala451Glu missense_variant 0.12
fbiC 1305421 p.Ala831Ser missense_variant 0.12
Rv1258c 1406478 p.Arg288Leu missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407283 p.Ala20Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473545 n.-113T>C upstream_gene_variant 0.12
fabG1 1673156 c.-284C>A upstream_gene_variant 0.15
fabG1 1673573 p.Thr45Ile missense_variant 0.11
fabG1 1673575 p.His46Asn missense_variant 0.12
fabG1 1673687 p.Glu83Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918037 p.Arg33Leu missense_variant 0.33
tlyA 1918684 c.745C>A synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221843 p.Arg441Gln missense_variant 0.14
Rv1979c 2222951 p.Val72Ile missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714542 p.Arg264Leu missense_variant 0.17
eis 2714768 p.Gly189Trp missense_variant 0.12
eis 2715480 c.-148C>A upstream_gene_variant 0.13
folC 2746195 c.1404C>A synonymous_variant 0.17
ribD 2987404 p.Arg189Leu missense_variant 0.12
thyX 3067978 c.-33C>A upstream_gene_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087791 c.972T>C synonymous_variant 0.1
fbiD 3339540 c.423C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474980 p.Arg325Leu missense_variant 0.17
whiB7 3568666 p.Thr5Ile missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613309 c.-193G>T upstream_gene_variant 0.17
fbiA 3640874 p.Thr111Asn missense_variant 0.12
alr 3840522 p.Ile300Asn missense_variant 0.12
clpC1 4038302 c.2403C>T synonymous_variant 0.12
clpC1 4040332 p.Val125Phe missense_variant 0.11
embC 4240425 p.Arg188Leu missense_variant 0.17
embC 4240946 p.Glu362* stop_gained 0.14
embC 4241327 p.Arg489Gly missense_variant 0.11
embA 4242505 c.-728G>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244973 p.Ala581Ser missense_variant 0.14
embB 4245617 c.-897C>A upstream_gene_variant 0.12
embB 4247716 c.1203C>A synonymous_variant 0.2
aftB 4267379 c.1458G>C synonymous_variant 0.11
aftB 4267380 c.1456delG frameshift_variant 0.11
aftB 4267541 p.Tyr432* stop_gained 0.15
aftB 4267629 p.Thr403Ile missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267880 c.957C>A synonymous_variant 0.15
aftB 4268363 p.Trp158* stop_gained 0.11
ubiA 4270005 c.-172C>A upstream_gene_variant 0.14
ubiA 4270033 c.-200C>A upstream_gene_variant 0.11
ethA 4326447 p.Gly343Trp missense_variant 0.11
ethA 4326869 p.Val202Gly 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 4407622 p.Asn194Ser missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0