TB-Profiler result

Run: SRR833101
Summary

Run ID: SRR833101

Sample name:

Date: 04-04-2023 21:05:09

Number of reads: 457594

Percentage reads mapped: 85.98

Strain: lineage4

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
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 761088 p.Ser428Gly missense_variant 0.33 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288955 p.Lys96Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5973 p.Lys245Thr missense_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491522 p.Arg247Leu missense_variant 0.25
ccsA 620722 p.Tyr278Asp missense_variant 1.0
rpoB 761620 p.Met605Arg missense_variant 0.4
rpoB 762277 p.Arg824Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766652 c.3285delC frameshift_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777148 p.Pro445Ala missense_variant 0.18
mmpS5 778581 p.Gly109Ser missense_variant 0.29
mmpL5 778678 c.-198C>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303666 p.Thr246Pro missense_variant 0.25
fbiC 1305169 p.Gln747Trp missense_variant 0.17
Rv1258c 1406889 p.Asn151Ser missense_variant 0.33
embR 1416445 p.Tyr301Leu missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475040 n.1383G>A non_coding_transcript_exon_variant 0.12
fabG1 1673270 c.-170G>A upstream_gene_variant 0.12
ndh 2102526 p.Phe173Val missense_variant 0.29
ndh 2102699 p.Leu115Pro missense_variant 0.2
ndh 2102709 p.Tyr112Asp missense_variant 0.18
katG 2156478 c.-367A>G upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518188 p.Ile25Asn missense_variant 0.12
kasA 2519305 c.1191A>C synonymous_variant 0.29
eis 2714563 p.Ile257Ser missense_variant 0.25
pepQ 2860491 c.-73C>A upstream_gene_variant 0.4
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064956 p.Ser412* stop_gained 0.5
Rv2752c 3065392 p.Val267Ala missense_variant 0.29
Rv2752c 3065418 c.774A>T synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3475194 p.Lys396Asn missense_variant 0.18
fbiA 3641488 p.Thr316Pro missense_variant 0.67
fbiA 3641495 p.Glu318Ala missense_variant 0.67
rpoA 3877943 c.564_565insG frameshift_variant 0.29
rpoA 3877946 p.Asp188His missense_variant 0.29
rpoA 3877953 p.Gln185His missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039456 p.Ala417Thr missense_variant 0.29
clpC1 4040613 p.Glu31Gly missense_variant 0.12
panD 4044277 p.Leu2Ser missense_variant 0.2
embC 4239732 c.-131T>A upstream_gene_variant 0.5
embC 4240131 p.Ala90Val missense_variant 0.67
embC 4240818 p.Thr319Lys missense_variant 0.5
embC 4240952 c.1092delT frameshift_variant 0.5
embB 4248134 p.Phe541Arg missense_variant 0.15
aftB 4268146 p.Tyr231Asp missense_variant 0.2
aftB 4268345 c.492C>A synonymous_variant 1.0
ubiA 4269308 p.Phe176Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407955 p.Arg83Gln missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0