TB-Profiler result

Run: SRR10525342
Summary

Run ID: SRR10525342

Sample name:

Date: 02-04-2023 18:31:05

Number of reads: 1691347

Percentage reads mapped: 98.39

Strain: lineage4.2.1;lineage4.1.2.1

Drug-resistance: Pre-XDR-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 1.0
lineage4.1 Euro-American T;X;H None 0.79
lineage4.2 Euro-American H;T;LAM None 0.19
lineage4.1.2 Euro-American T;H None 0.75
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.25
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.74
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
gyrA 7570 p.Ala90Val missense_variant 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.36 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.23 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.16 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 0.39 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid
pncA 2288955 p.Lys96Thr missense_variant 0.27 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 0.27 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.16
fgd1 491591 p.Lys270Met missense_variant 0.77
mshA 575679 p.Asn111Ser missense_variant 0.74
mshA 576108 p.Ala254Gly missense_variant 0.34
mshA 576513 p.Leu389Pro missense_variant 0.31
ccsA 619969 p.Val27Ile missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.79
rpoB 761267 c.1461C>T synonymous_variant 0.38
rpoB 761407 p.Val534Ala missense_variant 0.3
rpoC 765150 p.Gly594Glu missense_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.16
embR 1416607 c.741G>A synonymous_variant 0.56
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.69
ribD 2986827 c.-12G>A upstream_gene_variant 0.27
ald 3086742 c.-78A>C upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.13
rpoA 3878613 c.-106A>C upstream_gene_variant 0.22
rpoA 3878637 c.-130G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.77
embB 4246584 p.Arg24Pro missense_variant 0.28
embB 4249594 c.3081G>A synonymous_variant 0.29
ubiA 4269391 p.Val148Ala missense_variant 0.22
ethA 4327088 p.Leu129Arg missense_variant 0.17
ethA 4328376 c.-903G>C upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0