TB-Profiler result

Run: SRR5341218

Summary

Run ID: SRR5341218

Sample name:

Date: 04-04-2023 10:07:41

Number of reads: 693191

Percentage reads mapped: 99.74

Strain: lineage4.3.3

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 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289028 p.Cys72Arg missense_variant 1.0 pyrazinamide
pncA 2289199 p.Glu15* stop_gained 0.22 pyrazinamide
embB 4247429 p.Met306Val 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 5720 p.Gly161Trp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9567 p.Asp756Asn missense_variant 0.13
fgd1 491619 p.Gln279His missense_variant 0.22
mshA 575909 p.Leu188Val missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 761674 p.Gly623Val missense_variant 0.12
rpoB 762311 c.2505C>T synonymous_variant 0.12
rpoB 762619 p.Trp938Leu missense_variant 0.12
rpoC 763753 c.384C>T synonymous_variant 0.17
rpoC 764164 c.795C>A synonymous_variant 0.18
rpoC 764363 p.Gly332Ser missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767111 p.Leu1248Met missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777001 p.His494Asn missense_variant 0.12
mmpR5 778313 c.-677G>T upstream_gene_variant 0.12
mmpS5 779683 c.-778G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407517 c.-177G>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475203 n.1546G>T non_coding_transcript_exon_variant 0.2
fabG1 1673560 p.Lys41Leu missense_variant 0.17
inhA 1674153 c.-49G>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918684 c.745C>A synonymous_variant 0.11
ndh 2101752 c.1290delC frameshift_variant 0.2
PPE35 2167794 p.Ile940Asn missense_variant 0.11
PPE35 2167801 c.2811delT frameshift_variant 0.14
PPE35 2167806 p.Tyr936Ser missense_variant 0.13
PPE35 2168051 c.2562G>T synonymous_variant 0.2
PPE35 2170224 p.Ala130Asp missense_variant 0.18
Rv1979c 2222842 c.322dupG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714778 p.Gln185His missense_variant 0.14
ahpC 2726462 c.270A>G synonymous_variant 0.12
folC 2746332 p.Glu423* stop_gained 0.15
folC 2747171 p.Gly143Val missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086929 p.Ala37Glu missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Cys missense_variant 0.25
fprA 3475218 p.Asp404Glu missense_variant 0.18
whiB7 3568800 c.-121C>A upstream_gene_variant 0.15
fbiA 3640798 c.258delG frameshift_variant 0.11
rpoA 3878485 p.Thr8Ile missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embC 4242332 p.Gly824Trp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246043 p.Asp937Glu missense_variant 0.13
embB 4248640 c.2127C>T synonymous_variant 0.25
embB 4249560 p.Pro1016Gln missense_variant 0.14
aftB 4267699 c.1138C>T synonymous_variant 0.12
aftB 4269627 c.-791G>A upstream_gene_variant 1.0
ethR 4327288 c.-261T>A upstream_gene_variant 0.12
ethA 4327314 p.Arg54Cys missense_variant 0.12
whiB6 4338367 p.Leu52Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0