TB-Profiler result

Run: SRR7517752
Summary

Run ID: SRR7517752

Sample name:

Date: 04-04-2023 19:35:54

Number of reads: 1186677

Percentage reads mapped: 94.63

Strain: lineage2.2

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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 764724 p.Phe452Ser missense_variant 0.88 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 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 6980 p.Ala581Thr missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8249 c.948C>A synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491783 p.Arg334Leu missense_variant 0.5
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762679 p.Leu958Pro missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763753 c.384C>A synonymous_variant 0.29
rpoC 763841 p.Glu158* stop_gained 0.18
rpoC 764192 p.Glu275* stop_gained 0.22
rpoC 766424 p.Gly1019Cys missense_variant 0.17
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 776872 p.Glu537* stop_gained 0.4
mmpL5 777398 c.1083G>T synonymous_variant 0.21
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305094 p.His722Asn missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.67
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.5
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.5
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.67
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.67
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
inhA 1674936 c.735G>T synonymous_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834420 c.879C>A synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156246 c.-135C>T upstream_gene_variant 0.29
katG 2156268 c.-157G>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168474 c.2139C>A synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223340 c.-176T>C upstream_gene_variant 0.67
Rv1979c 2223360 c.-196G>T upstream_gene_variant 0.67
pncA 2289313 c.-72G>T upstream_gene_variant 0.18
pncA 2289735 c.-494C>A upstream_gene_variant 0.5
ahpC 2725994 c.-199G>T upstream_gene_variant 0.17
ahpC 2726192 c.-1C>A upstream_gene_variant 0.33
pepQ 2859600 c.819G>T synonymous_variant 0.5
pepQ 2859663 c.756G>A synonymous_variant 0.29
thyA 3074382 p.Phe30Leu missense_variant 0.29
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086890 p.Ala24Val missense_variant 0.25
ald 3087144 p.Asp109Tyr missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474717 c.711C>T synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841606 c.-186G>T upstream_gene_variant 0.29
rpoA 3877847 p.Leu221Met missense_variant 0.5
rpoA 3877917 p.Glu197Asp missense_variant 0.2
ddn 3986963 c.120C>A synonymous_variant 0.29
clpC1 4040476 p.His77Tyr missense_variant 0.5
embC 4241752 p.Leu630Phe missense_variant 0.18
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
embB 4249734 p.Pro1074His missense_variant 0.29
aftB 4267594 p.Ala415Thr missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269156 c.-320C>A upstream_gene_variant 0.4
ubiA 4269208 p.Ser209* stop_gained 0.4
aftB 4269456 c.-620G>T upstream_gene_variant 0.17
ethA 4326606 p.Asp290Tyr missense_variant 0.5
ethR 4326625 c.-924G>A upstream_gene_variant 0.75
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 1.0