TB-Profiler result

Run: ERR031461
Summary

Run ID: ERR031461

Sample name:

Date: 31-03-2023 08:26:41

Number of reads: 823912

Percentage reads mapped: 97.55

Strain: lineage4.3.4;lineage3.1;lineage2.2.1.1;lineage2.1

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 0.11
lineage2 East-Asian Beijing RD105 0.56
lineage4 Euro-American LAM;T;S;X;H None 0.1
lineage2.1 East-Asian (non-Beijing) None None 0.13
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.29
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.48
lineage4.3.4 Euro-American (LAM) LAM RD174 0.08
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.18
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
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid
embC 4240781 p.Ala307Thr missense_variant 0.12 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.21 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 8715 p.Pro472Ser missense_variant 0.29
gyrA 9143 c.1842T>C synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.96
mshA 575907 p.Ala187Val missense_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 0.38
rpoB 759746 c.-61C>T upstream_gene_variant 0.16
rpoC 762434 c.-936T>G upstream_gene_variant 0.28
rpoC 762695 c.-675C>T upstream_gene_variant 0.15
rpoB 762831 p.Ser1009Cys missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 764995 c.1626C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
mmpL5 776182 p.Asp767Asn missense_variant 0.64
mmpS5 779546 c.-641G>A upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801211 p.Gln135* stop_gained 0.12
fbiC 1305177 c.2247A>G synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
atpE 1460940 c.-105C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471777 n.-69C>A upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.83
katG 2155506 c.606C>A synonymous_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.22
pncA 2289102 p.Thr47Ile missense_variant 0.2
pncA 2289365 c.-125delC upstream_gene_variant 0.38
eis 2714662 p.Ala224Val missense_variant 0.12
eis 2714711 p.Pro208Thr missense_variant 0.14
eis 2714721 c.612C>T synonymous_variant 0.14
eis 2714846 p.Val163Ile missense_variant 0.36
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
ahpC 2726323 p.Pro44Arg missense_variant 0.25
pepQ 2859705 c.714G>A synonymous_variant 0.17
ribD 2986830 c.-9A>T upstream_gene_variant 0.14
thyA 3074305 p.Ala56Val missense_variant 0.14
ald 3086728 c.-92C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087518 c.699C>T synonymous_variant 0.36
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.45
rpoA 3878137 p.His124Arg missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.35
embA 4244220 c.988C>T synonymous_variant 0.15
embA 4244379 p.Pro383Ser missense_variant 0.17
embB 4248588 p.Gly692Asp missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.43
aftB 4268858 c.-22G>A upstream_gene_variant 0.27
ubiA 4269529 p.Ala102Gly 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 0.39
gid 4408156 p.Leu16Arg missense_variant 0.11