TB-Profiler result

Run: ERR4827935
Summary

Run ID: ERR4827935

Sample name:

Date: 01-04-2023 18:32:35

Number of reads: 4253996

Percentage reads mapped: 99.36

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 0.36
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.4
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 0.24 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.35 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.34 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid
eis 2715369 c.-37G>T upstream_gene_variant 0.51 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.38 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.32 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
gyrB 6446 p.Ala403Ser missense_variant 0.87
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.68
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.43
ccsA 620625 p.Ile245Met missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.53
Rv1258c 1406760 c.580_581insC frameshift_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155947 c.165T>G synonymous_variant 0.47
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 0.77
folC 2747433 c.166C>T synonymous_variant 0.8
pepQ 2860154 c.256_264delCGGGCCGGC conservative_inframe_deletion 0.51
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.45
Rv3083 3449022 c.519C>T synonymous_variant 0.81
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.54
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
alr 3840932 c.489C>T synonymous_variant 0.42
ddn 3986987 c.144G>T synonymous_variant 0.68
embC 4239843 c.-20A>C upstream_gene_variant 0.72
embC 4240671 p.Thr270Ile missense_variant 0.52
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.4
embA 4244220 c.988C>T synonymous_variant 0.5
embB 4247646 p.Glu378Ala missense_variant 0.58
aftB 4267647 p.Asp397Gly missense_variant 0.45
ubiA 4269387 p.Glu149Asp missense_variant 0.75
aftB 4269606 c.-770T>C upstream_gene_variant 0.72
whiB6 4338563 c.-42G>T upstream_gene_variant 0.44
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407684 p.Glu173Asp missense_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.22