TB-Profiler result

Run: ERR4827892
Summary

Run ID: ERR4827892

Sample name:

Date: 01-04-2023 18:27:57

Number of reads: 2264348

Percentage reads mapped: 99.52

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
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 5739 p.Thr167Met missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7565 c.264C>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8858 c.1557T>C synonymous_variant 0.13
gyrA 8867 c.1566A>G synonymous_variant 0.12
gyrA 8870 c.1569G>C synonymous_variant 0.12
gyrA 8873 c.1572A>C synonymous_variant 0.12
gyrA 8897 c.1596T>C synonymous_variant 0.12
gyrA 8903 c.1602T>C synonymous_variant 0.12
gyrA 8915 c.1614A>G synonymous_variant 0.12
gyrA 8939 c.1638T>C synonymous_variant 0.12
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 576089 p.Ala254Gly missense_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761537 c.1731C>G synonymous_variant 0.12
rpoB 761570 c.1764T>C synonymous_variant 0.12
rpoB 761573 c.1767C>G synonymous_variant 0.12
rpoB 761579 c.1773G>C synonymous_variant 0.12
rpoB 761606 c.1800C>G synonymous_variant 0.12
rpoB 761612 c.1806G>C synonymous_variant 0.11
rpoB 761615 c.1809A>C synonymous_variant 0.14
rpoB 761636 c.1830G>T synonymous_variant 0.11
rpoB 761645 c.1839C>G synonymous_variant 0.1
rpoB 761648 c.1842T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765317 p.Leu650Ile missense_variant 0.12
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
rpsL 781419 c.-141G>T upstream_gene_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475315 n.1662delG non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101856 c.1186delT frameshift_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155191 c.921A>C synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.16
PPE35 2167967 c.2646A>C synonymous_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.11
Rv1979c 2222418 p.Asp249Glu missense_variant 0.14
Rv1979c 2222465 p.Gly234Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
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
rpoA 3877939 p.Asp190Gly missense_variant 1.0
clpC1 4039069 p.Ser546Thr missense_variant 0.2
clpC1 4039410 p.Arg432His missense_variant 0.17
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
embA 4245834 c.2610_2612dupGGT disruptive_inframe_insertion 1.0
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.3
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.31
embB 4246567 c.54G>T synonymous_variant 0.31
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4249736 p.Pro1075Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269543 c.-707G>T upstream_gene_variant 0.12
ethA 4327253 p.Ala74Glu 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 4407927 p.Glu92Asp missense_variant 1.0
gid 4408165 p.Gly13Val missense_variant 0.15