TB-Profiler result

Run: SRR4035629

Summary

Run ID: SRR4035629

Sample name:

Date: 04-04-2023 07:13:35

Number of reads: 1345986

Percentage reads mapped: 99.7

Strain: lineage4.3.4.2.1

Drug-resistance: HR-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 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
katG 2154805 c.1306delC frameshift_variant 0.13 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 6502 c.-800T>C upstream_gene_variant 0.1
gyrA 6943 c.-359G>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8553 c.1255dupG frameshift_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575345 c.-2delG upstream_gene_variant 0.12
mshA 575651 c.307delG frameshift_variant 0.17
mshA 576231 p.Ile295Thr missense_variant 0.11
mshA 576425 p.Val360Met missense_variant 0.17
rpoB 761625 p.Arg607Ser missense_variant 0.18
rpoC 762548 c.-822C>T upstream_gene_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777962 c.519C>T synonymous_variant 0.11
mmpL5 778149 c.331delC frameshift_variant 0.12
mmpL5 778275 p.Ala69Val missense_variant 0.18
mmpL5 778516 c.-36C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303745 c.819_823dupGTTAC frameshift_variant 0.11
fbiC 1304006 p.Pro359Leu missense_variant 0.13
fbiC 1304378 p.Leu483Pro missense_variant 0.12
Rv1258c 1406566 p.Gln259* stop_gained 0.15
Rv1258c 1406936 c.405A>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471771 n.-74delG upstream_gene_variant 0.12
inhA 1673634 c.-568C>T upstream_gene_variant 0.14
inhA 1674952 p.Pro251Ala missense_variant 0.13
rpsA 1834407 p.Arg289His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102974 c.69G>A synonymous_variant 0.1
PPE35 2169320 p.Leu431Phe missense_variant 0.27
PPE35 2170529 c.84G>A synonymous_variant 0.13
Rv1979c 2222538 c.627C>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289170 c.72C>T synonymous_variant 0.12
pncA 2289175 p.Gly23Ser missense_variant 0.12
pncA 2289564 c.-323C>T upstream_gene_variant 0.14
kasA 2519065 c.951C>T synonymous_variant 0.15
eis 2714138 p.Ala399Thr missense_variant 0.14
eis 2714902 p.Arg144Gln missense_variant 0.11
eis 2715016 c.316delC frameshift_variant 0.15
ahpC 2726427 p.Asp79Tyr missense_variant 0.13
ahpC 2726740 p.Pro183Leu missense_variant 0.13
Rv2752c 3065652 c.540C>T synonymous_variant 0.11
Rv2752c 3066008 p.Pro62Ser missense_variant 0.11
thyA 3073745 p.Tyr243His missense_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074639 c.-168G>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.33
fbiD 3339469 p.Pro118Ser missense_variant 0.15
Rv3083 3448691 p.Gly63Asp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612150 p.Gln323* stop_gained 0.12
Rv3236c 3613202 c.-86G>A upstream_gene_variant 0.11
fbiA 3640562 p.Ala7Val missense_variant 0.11
fbiA 3641198 p.Ser219Asn missense_variant 0.12
fbiB 3642234 p.Arg234Trp missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840773 c.648C>T synonymous_variant 0.11
rpoA 3878415 c.92delG frameshift_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4040060 c.645C>T synonymous_variant 0.12
embC 4239955 p.Tyr31* stop_gained 0.1
embC 4241688 c.1829delG frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243959 c.730delG frameshift_variant 0.15
embA 4245125 c.1893G>T synonymous_variant 0.12
embA 4245374 c.2142G>A synonymous_variant 0.14
embA 4245462 p.Asp744Asn missense_variant 0.13
embB 4247673 p.Ala387Val missense_variant 0.11
aftB 4267325 c.1512G>T synonymous_variant 0.11
aftB 4267757 c.1079dupG frameshift_variant 0.18
aftB 4268078 c.759C>A synonymous_variant 0.14
aftB 4268457 p.Ala127Val missense_variant 0.12
aftB 4268459 c.376_377delAT frameshift_variant 0.12
aftB 4269012 c.-176G>T upstream_gene_variant 0.15
whiB6 4338286 c.235delG frameshift_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0