TB-Profiler result

Run: SRR12416829
Summary

Run ID: SRR12416829

Sample name:

Date: 03-04-2023 06:48:05

Number of reads: 5484039

Percentage reads mapped: 90.49

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 0.91 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.86 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.93 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155732 p.Gln127Pro missense_variant 0.97 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.95 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
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 0.98
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760223 c.417T>C synonymous_variant 0.15
rpoB 760235 c.429T>C synonymous_variant 0.15
rpoB 760283 c.477G>C synonymous_variant 0.14
rpoB 760298 c.492G>C synonymous_variant 0.14
rpoB 760328 c.522G>C synonymous_variant 0.13
rpoB 761015 c.1209G>C synonymous_variant 0.14
rpoB 761021 c.1215G>C synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764858 c.1489T>C synonymous_variant 0.15
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
fbiC 1302874 c.-57G>A upstream_gene_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.14
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.14
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.13
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.14
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rpsA 1833410 c.-132G>A upstream_gene_variant 1.0
rpsA 1833940 c.399C>G synonymous_variant 0.14
rpsA 1834012 c.471G>C synonymous_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834465 c.924T>C synonymous_variant 0.13
rpsA 1834468 c.927A>G synonymous_variant 0.13
rpsA 1834489 c.948T>C synonymous_variant 0.13
rpsA 1834495 c.954G>A synonymous_variant 0.13
rpsA 1834499 c.958C>T synonymous_variant 0.14
rpsA 1834528 c.987T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519206 c.1092C>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841614 c.-194C>G upstream_gene_variant 1.0
rpoA 3878076 c.432C>T synonymous_variant 0.13
rpoA 3878094 c.414C>G synonymous_variant 0.14
rpoA 3878103 c.405A>G synonymous_variant 0.15
rpoA 3878106 c.402G>C synonymous_variant 0.14
rpoA 3878193 c.315T>C synonymous_variant 0.13
rpoA 3878205 c.303T>C synonymous_variant 0.14
rpoA 3878217 c.291A>G synonymous_variant 0.16
rpoA 3878232 c.276G>C synonymous_variant 0.13
rpoA 3878247 c.261G>C synonymous_variant 0.15
rpoA 3878271 c.237T>C synonymous_variant 0.14
rpoA 3878276 c.232C>T synonymous_variant 0.14
rpoA 3878284 p.Glu75Ala missense_variant 0.13
rpoA 3878292 c.216T>C synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.16
rpoA 3878313 c.195G>T synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4248220 c.1707A>C synonymous_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.99
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