TB-Profiler result

Run: SRR16088240
Summary

Run ID: SRR16088240

Sample name:

Date: 03-04-2023 16:05:06

Number of reads: 3723890

Percentage reads mapped: 99.62

Strain: lineage4.1.2.1;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 0.58
lineage4 Euro-American LAM;T;S;X;H None 0.45
lineage4.1 Euro-American T;X;H None 0.42
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.58
lineage4.1.2 Euro-American T;H None 0.42
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.58
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.15
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 761109 p.Asp435Phe missense_variant 0.16 rifampicin
rpoB 761141 p.His445Gln missense_variant 0.2 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.52 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.6 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.62 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid
embB 4247730 p.Gly406Ala missense_variant 0.63 ethambutol
ethR 4327876 p.Phe110Leu missense_variant 0.24 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 0.99
fgd1 491591 p.Lys270Met missense_variant 0.46
fgd1 491742 c.960T>C synonymous_variant 0.6
mshA 575679 p.Asn111Ser missense_variant 0.19
mshA 576108 p.Ala254Gly missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.55
rpoB 759841 p.Ser12Thr missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 0.44
rpoC 763031 c.-339T>C upstream_gene_variant 0.59
rpoC 765150 p.Gly594Glu missense_variant 0.39
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.6
mmpL5 777883 p.Gly200Arg missense_variant 0.16
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.33
Rv1258c 1406760 c.580_581insC frameshift_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.56
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 0.64
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.56
katG 2155259 p.Gly285Cys missense_variant 0.59
PPE35 2167926 p.Leu896Ser missense_variant 0.59
PPE35 2168303 c.2310G>T synonymous_variant 0.32
PPE35 2169776 p.Phe279Leu missense_variant 0.31
PPE35 2170065 p.Ala183Gly missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612770 p.Val116Ala missense_variant 0.65
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68
alr 3840263 c.1158C>T synonymous_variant 0.31
rpoA 3878641 c.-134C>G upstream_gene_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.4
embA 4243460 c.228C>T synonymous_variant 0.61
embB 4246527 p.Ala5Gly missense_variant 0.21
embB 4246529 p.Ser6Arg missense_variant 0.33
embB 4247086 c.573C>T synonymous_variant 0.31
aftB 4267647 p.Asp397Gly missense_variant 0.45
ubiA 4269847 c.-14A>G upstream_gene_variant 0.24
ethA 4326676 p.Ser266Arg missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.66
gid 4407654 c.549G>A synonymous_variant 0.66
gid 4407927 p.Glu92Asp missense_variant 0.63