TB-Profiler result

Run: SRR11972432

Summary

Run ID: SRR11972432

Sample name:

Date: 03-04-2023 05:42:07

Number of reads: 1029130

Percentage reads mapped: 64.93

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 0.99
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 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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
gyrB 5861 p.Leu208Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8764 p.Asp488Val missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491617 p.Gln279Lys missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619955 p.Val22Ala missense_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763501 p.Asp44Glu missense_variant 0.97
rpoC 764541 p.Val391Gly missense_variant 0.17
rpoC 764543 p.Thr392Asp missense_variant 0.17
rpoC 765462 p.Asn698Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775673 p.Trp936Cys missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778740 p.Val56Leu missense_variant 0.12
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
atpE 1461077 c.35delG frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.12
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.12
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.13
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.13
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.13
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.12
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.1
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.14
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.11
rrl 1474852 n.1195T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
fabG1 1674019 p.Leu194Met missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155111 p.Glu334Gly missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.93
PPE35 2167955 c.2658A>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288743 p.Thr167Ala missense_variant 0.17
pncA 2289741 c.-501dupG upstream_gene_variant 1.0
folC 2747686 c.-88C>A upstream_gene_variant 0.15
pepQ 2859320 c.1098delC frameshift_variant 0.12
thyA 3074336 p.Thr46Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 0.88
Rv3083 3449738 p.His412Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568735 c.-56G>A upstream_gene_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038495 p.Arg737Gln missense_variant 0.14
embC 4240648 c.786C>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.22
embB 4249676 p.Arg1055Cys missense_variant 0.2
embB 4249738 c.3225C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326347 p.Gly376Asp missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.94