TB-Profiler result

Run: SRR6785501
Summary

Run ID: SRR6785501

Sample name:

Date: 04-04-2023 16:00:47

Number of reads: 1627579

Percentage reads mapped: 99.55

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide
ethA 4326855 p.Arg207Gly missense_variant 1.0 ethionamide
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 9174 p.Leu625Met missense_variant 0.13
gyrA 9254 c.1953C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 765774 p.Ile802Thr missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473675 n.18C>T non_coding_transcript_exon_variant 0.12
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.17
rrl 1474250 n.593A>G non_coding_transcript_exon_variant 0.1
rrl 1475344 n.1687G>T non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102142 p.Gly301Cys missense_variant 0.12
ndh 2102166 p.Ser293Pro missense_variant 0.12
katG 2153967 p.Asp715Glu missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168466 c.2146dupC frameshift_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065763 p.Tyr143* stop_gained 1.0
Rv2752c 3066153 c.39C>T synonymous_variant 0.13
thyX 3067582 p.Met122Val missense_variant 0.11
thyX 3067652 c.294T>C synonymous_variant 0.12
thyA 3073715 p.Pro253Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087895 p.Leu359Pro missense_variant 0.17
Rv3083 3448840 p.Gln113Lys missense_variant 0.15
Rv3083 3448899 c.396C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612399 p.Ala240Thr missense_variant 0.12
Rv3236c 3612404 p.Ala238Gly missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245035 c.1803C>A synonymous_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247516 p.Asn335Asp missense_variant 0.11
embB 4247840 p.Gly443Ser missense_variant 0.13
embB 4249744 c.3231G>A synonymous_variant 0.14
embB 4249751 c.3238T>C synonymous_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268619 c.217delG frameshift_variant 0.12
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