TB-Profiler result

Run: SRR1165643
Summary

Run ID: SRR1165643

Sample name:

Date: 03-04-2023 00:56:31

Number of reads: 4726374

Percentage reads mapped: 99.23

Strain: lineage4.3.4.2

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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.65
lineage4.4.1.1 Euro-American S;Orphans None 0.37
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.63
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 761140 p.His445Leu missense_variant 0.63 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 0.18 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.18 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.53 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.72 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
gyrB 6140 p.Val301Leu missense_variant 0.66
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 490682 c.-101C>T upstream_gene_variant 0.15
mshA 575538 p.Asp64Gly missense_variant 0.67
rpoC 764744 p.Arg459Trp missense_variant 0.61
rpoC 764995 c.1626C>G synonymous_variant 0.73
rpoC 765494 p.Val709Leu missense_variant 0.61
rpoC 766487 p.Pro1040Ser missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.31
PPE35 2169840 p.Gly258Asp missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859608 p.Arg271Gly missense_variant 0.29
ribD 2986827 c.-12G>A upstream_gene_variant 0.39
Rv2752c 3064993 p.Trp400* stop_gained 0.48
thyA 3073868 p.Thr202Ala missense_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 0.5
Rv3083 3448608 c.105G>A synonymous_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.77
Rv3236c 3612665 p.Val151Ala missense_variant 0.29
fbiB 3641358 c.-177G>T upstream_gene_variant 0.25
fbiA 3641439 c.900_901dupGG frameshift_variant 0.18
fbiB 3642294 c.764_767dupAAGC frameshift_variant 0.4
alr 3840719 c.702A>G synonymous_variant 0.66
clpC1 4038287 c.2418C>T synonymous_variant 0.56
ubiA 4269308 p.Phe176Leu missense_variant 0.4
ethA 4326853 c.612_620dupGCTGCAGCG disruptive_inframe_insertion 0.48
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 p.Lys163Asn missense_variant 0.55
gid 4408156 p.Leu16Arg missense_variant 0.5