TB-Profiler result

Run: SRR5341217
Summary

Run ID: SRR5341217

Sample name:

Date: 04-04-2023 10:07:24

Number of reads: 323448

Percentage reads mapped: 98.9

Strain: lineage4.1.2

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 1.0
lineage4.1.2 Euro-American T;H None 0.91
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 0.33 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 490639 c.-144C>A upstream_gene_variant 0.13
fgd1 490758 c.-25T>G upstream_gene_variant 0.25
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.33
ccsA 619717 c.-174G>A upstream_gene_variant 0.29
ccsA 620611 p.Gly241Ser missense_variant 0.22
ccsA 620654 p.Trp255* stop_gained 0.2
rpoB 760115 c.309C>T synonymous_variant 0.83
rpoB 763134 p.Gly1110Cys missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpR5 778469 c.-521T>C upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304826 c.1900delT frameshift_variant 0.17
fbiC 1305238 p.His770Asn missense_variant 0.25
Rv1258c 1406252 c.1088delG frameshift_variant 0.29
Rv1258c 1406451 p.Thr297Asn missense_variant 0.2
rrl 1473580 n.-78G>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154143 p.Phe657Leu missense_variant 0.22
PPE35 2168014 p.Ala867Thr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
Rv1979c 2221747 p.Arg473Gln missense_variant 0.21
Rv1979c 2223291 c.-127G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.83
eis 2715436 c.-104G>A upstream_gene_variant 0.22
ahpC 2726341 p.Val50Gly missense_variant 0.33
folC 2746745 p.Val285Gly missense_variant 0.5
pepQ 2860023 c.396C>T synonymous_variant 0.5
Rv2752c 3066175 p.Pro6His missense_variant 0.29
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.4
thyA 3074316 p.Phe52Leu missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339143 c.28_35delATCGGCTT frameshift_variant 0.22
fbiD 3339156 c.40_41insAGCCGATA frameshift_variant 0.2
Rv3083 3448569 c.66C>T synonymous_variant 0.29
Rv3083 3449566 p.Gly355Arg missense_variant 1.0
Rv3083 3449759 p.Thr419Met missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3640773 c.-762C>T upstream_gene_variant 0.15
fbiA 3640880 c.340dupG frameshift_variant 0.2
fbiA 3640888 c.349delC frameshift_variant 0.22
alr 3840764 c.657G>T synonymous_variant 0.29
panD 4043868 c.414G>T synonymous_variant 0.33
embC 4239906 p.Pro15Leu missense_variant 0.2
embC 4239993 p.Ala44Asp missense_variant 0.33
embC 4241473 c.1611G>T synonymous_variant 0.33
embC 4241615 p.Lys585* stop_gained 0.33
embC 4242329 p.Glu823Lys missense_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243494 c.262C>T synonymous_variant 0.15
embA 4244008 p.Ala259Glu missense_variant 0.33
embA 4244055 p.Gly275Arg missense_variant 0.29
embB 4248226 c.1713G>T synonymous_variant 0.29
embB 4249621 c.3108G>T synonymous_variant 0.25
aftB 4267437 p.Arg467Gln missense_variant 0.22
aftB 4267449 p.Val463Glu missense_variant 0.22
ethA 4327728 c.-255C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.2