TB-Profiler result

Run: ERR11043505

Summary

Run ID: ERR11043505

Sample name:

Date: 31-03-2023 11:35:41

Number of reads: 5316411

Percentage reads mapped: 99.47

Strain: lineage5;lineage4.2.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.86
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.12
lineage4.2 Euro-American H;T;LAM None 0.85
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.85
lineage4.2.2.1 Euro-American LAM7-TUR None 0.86
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 761095 p.Leu430Pro missense_variant 0.11 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.12 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin
rrs 1473183 n.1338A>C non_coding_transcript_exon_variant 0.11 aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid
pncA 2289028 p.Cys72Arg missense_variant 0.2 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 0.15 isoniazid
embB 4248002 p.Gln497Lys missense_variant 0.86 ethambutol
gid 4407944 c.258_259insG frameshift_variant 0.82 streptomycin
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 6446 p.Ala403Ser missense_variant 0.16
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.19
mshA 576077 c.730C>T synonymous_variant 0.88
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoB 760677 p.Glu291Lys missense_variant 0.17
rpoB 760994 c.1188G>A synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.15
eis 2714510 c.823T>C synonymous_variant 0.15
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.84
ald 3086742 c.-78A>C upstream_gene_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339000 c.-117_-116delCA upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840932 c.489C>T synonymous_variant 0.13
ddn 3986987 c.144G>T synonymous_variant 0.12
ddn 3987180 p.Asp113Asn missense_variant 0.12
clpC1 4040824 c.-120C>T upstream_gene_variant 0.15
embC 4239843 c.-20A>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.13
embA 4245147 p.Pro639Ser missense_variant 0.16
embB 4246584 p.Arg24Pro missense_variant 0.22
embB 4247465 p.Asn318Asp missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 0.17
embB 4248616 c.2103G>T synonymous_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 0.18
aftB 4269606 c.-770T>C upstream_gene_variant 0.16
ethA 4326533 p.Thr314Ile missense_variant 0.88
ethA 4326977 p.His166Pro missense_variant 0.11
ethA 4327103 p.Gly124Asp missense_variant 0.18
ethA 4328322 c.-849G>T upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407947 p.Leu86Phe missense_variant 0.19