TB-Profiler result

Run: ERR234566
Summary

Run ID: ERR234566

Sample name:

Date: 31-03-2023 18:05:40

Number of reads: 3185813

Percentage reads mapped: 99.62

Strain: lineage4.8;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 0.49
lineage4 Euro-American LAM;T;S;X;H None 0.52
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.49
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.49
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.44
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 0.23 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
pncA 2289103 p.Thr47Ala missense_variant 0.37 pyrazinamide
pncA 2289222 p.Val7Gly missense_variant 0.18 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.24 kanamycin
embB 4247399 p.Asn296His missense_variant 0.25 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.18 ethambutol
ethA 4326707 p.Trp256* stop_gained 0.14 ethionamide
ethA 4327363 c.110delA frameshift_variant 0.3 ethionamide, 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 0.59
gyrA 9304 p.Gly668Asp missense_variant 0.48
fgd1 491742 c.960T>C synonymous_variant 0.3
mshA 575907 p.Ala187Val missense_variant 0.56
ccsA 620625 p.Ile245Met missense_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.52
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpL5 776182 p.Asp767Asn missense_variant 0.57
mmpL5 778107 p.Ser125Cys missense_variant 0.39
mmpS5 779615 c.-710C>G upstream_gene_variant 0.45
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.54
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.51
inhA 1673406 c.-796C>T upstream_gene_variant 0.24
rpsA 1834177 c.636A>C synonymous_variant 0.4
rpsA 1834427 p.Ile296Phe missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.54
PPE35 2167926 p.Leu896Ser missense_variant 0.32
PPE35 2168149 p.Pro822Ser missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.39
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
rpoA 3877949 p.Thr187Ala missense_variant 0.23
clpC1 4038857 c.1848C>A synonymous_variant 0.22
embC 4242425 p.Arg855Gly missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.35
embA 4243460 c.228C>T synonymous_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.41
ubiA 4269298 p.Ile179Thr missense_variant 0.17
ethA 4328378 c.-905G>C upstream_gene_variant 0.59
whiB6 4338371 p.Thr51Pro missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.53
gid 4407927 p.Glu92Asp missense_variant 0.44