TB-Profiler result

Run: ERR5866115
Summary

Run ID: ERR5866115

Sample name:

Date: 02-04-2023 00:30:52

Number of reads: 768341

Percentage reads mapped: 98.79

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 0.99
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 2288853 p.Val130Gly missense_variant 1.0 pyrazinamide
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491295 c.513C>G synonymous_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761572 p.Pro589Leu missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764822 p.Asp485Tyr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775676 c.2805G>A synonymous_variant 0.13
mmpL5 776013 p.Trp823Leu missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779485 c.496T>C stop_lost&splice_region_variant 0.17
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
embR 1417523 c.-177delG upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834635 p.Ala365Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918501 p.Gly188Trp missense_variant 0.13
ndh 2101920 p.Arg375Gly missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.21
PPE35 2170446 p.Ser56* stop_gained 0.14
PPE35 2170454 c.159C>G synonymous_variant 0.14
PPE35 2170457 c.156G>C synonymous_variant 0.15
PPE35 2170460 c.153G>A synonymous_variant 0.17
PPE35 2170465 p.Ala50Ser missense_variant 0.18
PPE35 2170472 c.141G>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290230 c.-989T>C upstream_gene_variant 0.25
ribD 2987439 p.Thr201Ala missense_variant 0.1
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087117 p.Ser100Thr missense_variant 0.14
Rv3083 3449314 p.Trp271Arg missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611977 c.1140C>A synonymous_variant 0.2
Rv3236c 3612682 c.435C>T synonymous_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.23
ddn 3986739 c.-105T>C upstream_gene_variant 0.15
embC 4241661 c.1804delG frameshift_variant 0.5
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 4243570 p.Thr113Lys missense_variant 0.11
embA 4243991 c.759T>A synonymous_variant 0.15
embB 4248492 p.Met660Thr missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268917 c.-81C>T upstream_gene_variant 1.0
ubiA 4269296 p.Met180Val missense_variant 1.0
ethA 4327830 c.-357G>T upstream_gene_variant 0.13
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