TB-Profiler result

Run: ERR4827422
Summary

Run ID: ERR4827422

Sample name:

Date: 01-04-2023 18:01:50

Number of reads: 553044

Percentage reads mapped: 99.43

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 0.99
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 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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 8625 p.Arg442Gly missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491126 p.Ala115Asp missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619761 c.-130G>A upstream_gene_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764368 c.999C>T synonymous_variant 0.33
rpoC 765065 p.Leu566Val missense_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 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
fbiC 1303540 p.Leu204Phe missense_variant 0.22
fbiC 1303555 p.Pro209Ala missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472680 n.835C>A non_coding_transcript_exon_variant 0.12
rrl 1474025 n.368T>A non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.45
fabG1 1674085 p.Glu216Lys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834384 c.843A>G synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.12
PPE35 2169491 c.1122T>C synonymous_variant 0.12
PPE35 2169732 p.Asn294Ser missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170147 p.Ser156Ala missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518681 c.567C>T synonymous_variant 0.2
folC 2746438 c.1161G>T synonymous_variant 0.18
folC 2746880 p.Lys240Arg missense_variant 0.14
pepQ 2859721 p.Met233Thr missense_variant 0.15
Rv2752c 3065484 c.708G>A synonymous_variant 0.17
thyA 3074393 p.Arg27Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087658 p.Pro280Leu missense_variant 0.12
ald 3087773 p.Met318Ile missense_variant 0.33
Rv3083 3448563 c.61delT frameshift_variant 0.25
Rv3083 3448574 c.71_72insA frameshift_variant 0.25
Rv3083 3449407 p.Asn302Asp missense_variant 0.18
Rv3083 3449554 p.Gln351Lys missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4239821 c.-42C>A upstream_gene_variant 0.17
embC 4241810 p.Trp650Arg missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244187 p.Thr319Ser missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247470 c.957T>C synonymous_variant 0.2
embB 4247472 p.Phe320Tyr missense_variant 0.2
embB 4248730 c.2219_2220delTG frameshift_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338476 p.Trp16Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.86