TB-Profiler result

Run: ERR5864127
Summary

Run ID: ERR5864127

Sample name:

Date: 01-04-2023 23:08:24

Number of reads: 1247271

Percentage reads mapped: 99.1

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
pncA 2289072 p.His57Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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 8149 p.Phe283Tyr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491385 p.Glu201Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576140 p.Glu265* stop_gained 0.11
mshA 576662 p.Ala439Thr missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760142 c.336C>A synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764242 c.873C>T synonymous_variant 0.13
rpoC 765113 p.Val582Leu missense_variant 0.52
rpoC 765334 c.1965C>G synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776127 c.2352_2353dupCT frameshift_variant 0.13
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776695 p.Val596Phe missense_variant 0.12
mmpL5 777492 p.Pro330Leu missense_variant 0.12
mmpR5 779078 p.Arg30Met missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303753 p.His275Tyr missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476761 n.3104G>C non_coding_transcript_exon_variant 0.1
rrl 1476782 n.3129delA non_coding_transcript_exon_variant 0.11
fabG1 1673731 p.Met98Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102847 p.Gly66* stop_gained 0.12
katG 2153939 p.Val725Ile missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155390 p.Pro241Leu missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169610 p.Gly335Cys missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170213 p.Ala134Thr missense_variant 0.18
PPE35 2170438 p.Gly59Cys missense_variant 0.15
PPE35 2170535 c.78G>A synonymous_variant 0.14
PPE35 2170547 c.66A>T synonymous_variant 0.12
Rv1979c 2222893 p.Gly91Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519244 p.Asp377Val missense_variant 0.13
ahpC 2726345 c.157delT frameshift_variant 0.11
folC 2746982 p.Gly206Asp missense_variant 0.11
Rv2752c 3065364 c.828G>T synonymous_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448327 c.-177C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641893 p.Leu120Pro missense_variant 0.11
alr 3841465 c.-45G>T upstream_gene_variant 0.13
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 4244177 c.945G>T synonymous_variant 0.14
embB 4246706 p.Gly65Arg missense_variant 0.13
embB 4246809 p.Leu99Pro missense_variant 0.12
embB 4246816 c.303C>T synonymous_variant 0.11
embB 4246916 p.Val135Leu missense_variant 0.12
embB 4247570 p.Pro353Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4328148 c.-675C>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 4407654 c.549G>A synonymous_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 1.0