TB-Profiler result

Run: ERR3639724
Summary

Run ID: ERR3639724

Sample name:

Date: 01-04-2023 02:41:10

Number of reads: 886098

Percentage reads mapped: 99.59

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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 761101 p.Gln432Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288703 p.Val180Gly missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620652 c.763delT frameshift_variant 0.29
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775649 c.2832G>A synonymous_variant 0.13
mmpL5 775996 p.Ile829Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406388 p.Cys318Tyr missense_variant 0.18
Rv1258c 1406825 c.516C>T synonymous_variant 0.12
Rv1258c 1406977 p.Thr122Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.1
kasA 2519153 p.Ile347Val missense_variant 0.11
pepQ 2859973 p.Ala149Val missense_variant 0.15
thyX 3067348 p.Ala200Thr missense_variant 0.12
fbiD 3339342 c.225G>A synonymous_variant 0.18
fbiD 3339431 p.Glu105Gly missense_variant 0.18
fprA 3474402 c.396C>T synonymous_variant 0.15
fbiB 3640974 c.-561T>G upstream_gene_variant 1.0
clpC1 4038433 c.2272C>T synonymous_variant 0.2
embC 4239700 c.-163A>T upstream_gene_variant 0.13
embC 4240598 p.Val246Met missense_variant 0.13
embC 4241515 c.1653G>A synonymous_variant 0.18
embC 4241699 p.Met613Val missense_variant 1.0
embC 4241868 p.Thr669Met missense_variant 0.15
embC 4241873 c.2011C>T synonymous_variant 0.15
embC 4241935 c.2073C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242886 c.-347G>A upstream_gene_variant 0.13
embA 4243489 p.Gly86Asp missense_variant 0.5
embA 4243847 c.615C>T synonymous_variant 0.22
embA 4243948 p.Arg239Gln missense_variant 0.14
embA 4244436 p.Leu402Phe missense_variant 0.12
embA 4244944 p.Ala571Val missense_variant 0.18
embA 4245102 p.Trp624Arg missense_variant 0.11
embA 4245373 p.Pro714Leu missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246602 p.Ala30Val missense_variant 0.14
embB 4246771 c.258C>T synonymous_variant 0.2
embB 4246812 p.Gly100Asp missense_variant 0.2
embB 4247073 p.Gly187Ala missense_variant 0.12
whiB6 4338234 c.288A>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0