TB-Profiler result

Run: ERR2229084

Summary

Run ID: ERR2229084

Sample name:

Date: 20-10-2023 20:21:00

Number of reads: 1528554

Percentage reads mapped: 93.11

Strain: lineage4.8

Drug-resistance: Sensitive


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 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
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 6811 c.-491C>T upstream_gene_variant 0.21
gyrA 6841 c.-461T>C upstream_gene_variant 0.17
gyrA 6844 c.-458T>C upstream_gene_variant 0.17
gyrA 6853 c.-449A>G upstream_gene_variant 0.17
gyrA 6856 c.-446T>C upstream_gene_variant 0.17
gyrA 6859 c.-443T>C upstream_gene_variant 0.16
gyrA 6862 c.-440C>G upstream_gene_variant 0.16
gyrA 6868 c.-434G>C upstream_gene_variant 0.14
gyrA 6901 c.-401G>C upstream_gene_variant 0.14
gyrA 6904 c.-398C>G upstream_gene_variant 0.14
gyrA 6949 c.-353A>G upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 760283 c.477G>C synonymous_variant 0.14
rpoB 760340 c.534G>T synonymous_variant 0.14
rpoB 760869 p.Val355Ile missense_variant 0.2
rpoB 762014 c.2208C>T synonymous_variant 0.2
rpoB 762017 c.2211A>G synonymous_variant 0.2
rpoC 762989 c.-381G>C upstream_gene_variant 0.23
rpoC 762995 c.-375G>T upstream_gene_variant 0.22
rpoC 763402 c.33C>G synonymous_variant 0.13
rpoC 763441 c.72C>T synonymous_variant 0.16
rpoC 763444 c.75T>C synonymous_variant 0.16
rpoC 763456 c.87A>G synonymous_variant 0.17
rpoC 763765 c.396T>C synonymous_variant 0.31
rpoC 763774 c.405G>C synonymous_variant 0.34
rpoC 763807 c.438T>C synonymous_variant 0.34
rpoC 763816 c.447C>G synonymous_variant 0.36
rpoC 763835 p.Ala156Met missense_variant 0.37
rpoC 763853 p.Val162Ile missense_variant 0.29
rpoC 763858 c.489A>G synonymous_variant 0.25
rpoC 763872 p.Gly168Ala missense_variant 0.21
rpoC 763876 p.Glu169Asp missense_variant 0.21
rpoC 763879 c.510A>G synonymous_variant 0.2
rpoC 763900 c.531G>C synonymous_variant 0.24
rpoC 765580 c.2211G>C synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781715 c.156T>C synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
fabG1 1673641 p.Val68Ile missense_variant 0.21
inhA 1673646 c.-556T>C upstream_gene_variant 0.21
fabG1 1673657 p.Thr73Lys missense_variant 0.22
inhA 1673660 c.-542C>A upstream_gene_variant 0.22
inhA 1673664 c.-538A>C upstream_gene_variant 0.19
inhA 1673667 c.-535A>G upstream_gene_variant 0.19
inhA 1673679 c.-523T>C upstream_gene_variant 0.18
inhA 1673685 c.-517C>T upstream_gene_variant 0.18
fabG1 1673710 p.Leu91Ile missense_variant 0.23
rpsA 1833874 c.333T>C synonymous_variant 0.33
rpsA 1834348 c.807T>C synonymous_variant 0.26
rpsA 1834546 c.1005T>C synonymous_variant 0.32
rpsA 1834609 c.1068T>C synonymous_variant 0.26
rpsA 1834618 c.1077G>C synonymous_variant 0.26
rpsA 1834633 c.1092A>G synonymous_variant 0.22
rpsA 1834639 c.1098T>C synonymous_variant 0.22
rpsA 1834654 p.Glu371Asp missense_variant 0.39
rpsA 1834684 c.1143C>T synonymous_variant 0.35
rpsA 1834690 c.1149T>C synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
clpC1 4039097 c.1608G>C synonymous_variant 0.25
clpC1 4039610 c.1095G>C synonymous_variant 0.19
clpC1 4039616 c.1089G>C synonymous_variant 0.19
clpC1 4039622 c.1083C>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247914 c.1401G>C synonymous_variant 0.29
embB 4247932 c.1419C>G synonymous_variant 0.26
embB 4247940 p.Leu476Trp missense_variant 0.26
embB 4247945 c.1432T>C synonymous_variant 0.26
embB 4247951 p.Ser480Ala missense_variant 0.25
embB 4247956 c.1443G>C synonymous_variant 0.25
embB 4247974 c.1461C>G synonymous_variant 0.16
embB 4248097 c.1584C>G synonymous_variant 0.16
embB 4248130 c.1617G>C synonymous_variant 0.15
embB 4248172 c.1659G>C synonymous_variant 0.17
embB 4248199 c.1686A>G synonymous_variant 0.14
embB 4248200 p.Ile563Val missense_variant 0.14
embB 4248205 c.1692C>G synonymous_variant 0.13
embB 4248206 p.Ser565Gly missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0