TB-Profiler result

Run: ERR2516138
Summary

Run ID: ERR2516138

Sample name:

Date: 31-03-2023 21:18:52

Number of reads: 758869

Percentage reads mapped: 99.58

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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326705 c.768delG 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 490704 c.-79A>G upstream_gene_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576763 p.Trp472Cys missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762344 c.2542delT frameshift_variant 0.12
rpoB 762442 p.Leu879Pro missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777612 p.Gly290Val missense_variant 0.15
mmpL5 777922 p.Thr187Ala missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304268 c.1338G>T synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407077 c.263dupG frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476424 n.2767G>T 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
katG 2153895 c.2217G>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170126 p.Val163Leu missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288853 c.380_388dupAGGTCGATG conservative_inframe_insertion 1.0
kasA 2518348 c.234A>T synonymous_variant 0.13
ald 3086695 c.-125C>T 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
fprA 3474525 p.Leu173Phe missense_variant 0.14
fprA 3474607 p.Gly201Ser missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642744 p.Ala404Ser missense_variant 0.12
rpoA 3877960 p.Val183Ala missense_variant 1.0
rpoA 3878677 c.-170C>A upstream_gene_variant 0.22
clpC1 4038162 p.Arg848Leu missense_variant 0.15
clpC1 4039146 p.Gly520Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249718 p.Thr1069Ala missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268459 c.376_377delAT frameshift_variant 0.14
aftB 4268618 c.219G>T synonymous_variant 0.29
ethA 4327329 p.Arg49Gly missense_variant 0.11
whiB6 4338563 c.-42G>T upstream_gene_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