TB-Profiler result

Run: ERR4828642
Summary

Run ID: ERR4828642

Sample name:

Date: 01-04-2023 19:00:12

Number of reads: 877978

Percentage reads mapped: 53.5

Strain: lineage2.2.1

Drug-resistance: HR-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 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.94
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
rpsL 781822 p.Lys88Arg missense_variant 0.9 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.94 isoniazid
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 575907 p.Ala187Val missense_variant 0.88
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760488 p.Val228Ile missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_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 0.91
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303326 c.396C>T synonymous_variant 0.95
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.33
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.29
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.29
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.29
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.25
rrl 1473940 n.283A>T non_coding_transcript_exon_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 0.95
rpsA 1834538 p.Val333Met missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168100 c.2512delC frameshift_variant 0.13
PPE35 2169438 p.Phe392Tyr missense_variant 0.18
Rv1979c 2222357 p.Thr270Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.11
Rv2752c 3065404 p.Gly263Asp missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448919 p.Cys139Tyr missense_variant 0.12
fprA 3473810 c.-197A>G upstream_gene_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.93
embC 4240671 p.Thr270Ile missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.88
embA 4244096 c.864C>T synonymous_variant 0.16
aftB 4267081 c.1756C>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326073 c.1401C>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.96