TB-Profiler result

Run: ERR161149
Summary

Run ID: ERR161149

Sample name:

Date: 20-10-2023 22:10:54

Number of reads: 2987848

Percentage reads mapped: 92.32

Strain: lineage4.3.4.2.1

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
lineage4.3 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 0.98
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
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 0.89
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762131 c.2325C>G synonymous_variant 0.14
rpoB 762143 c.2337T>C synonymous_variant 0.18
rpoB 762149 c.2343G>C synonymous_variant 0.18
rpoB 762176 c.2370T>C synonymous_variant 0.17
rpoB 762185 c.2379G>C synonymous_variant 0.16
rpoB 762197 c.2391C>T synonymous_variant 0.18
rpoB 762489 p.Val895Leu missense_variant 0.12
rpoC 764188 c.819A>G synonymous_variant 0.12
rpoC 764203 c.834G>T synonymous_variant 0.15
rpoC 764206 c.837T>C synonymous_variant 0.15
rpoC 764213 p.Arg282Lys missense_variant 0.15
rpoC 764257 c.888G>C synonymous_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765658 c.2289C>T synonymous_variant 0.12
rpoC 765784 c.2415C>G synonymous_variant 0.12
rpoC 765811 c.2442T>G synonymous_variant 0.15
rpoC 765826 c.2457T>C synonymous_variant 0.13
rpoC 767119 c.3750A>G synonymous_variant 0.14
rpoC 767134 c.3765C>A synonymous_variant 0.13
rpoC 767158 c.3789T>C synonymous_variant 0.13
rpoC 767167 c.3798C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.18
rpsA 1833703 c.162C>T synonymous_variant 0.14
rpsA 1833724 c.183C>G synonymous_variant 0.15
rpsA 1833727 c.186G>T synonymous_variant 0.14
rpsA 1834021 c.480C>T synonymous_variant 0.14
rpsA 1834030 c.489C>G synonymous_variant 0.14
rpsA 1834249 c.708T>C synonymous_variant 0.16
rpsA 1834261 c.720A>G synonymous_variant 0.13
rpsA 1834264 c.723G>C synonymous_variant 0.13
rpsA 1834294 c.753G>C synonymous_variant 0.14
rpsA 1834303 c.762T>C synonymous_variant 0.14
rpsA 1834612 c.1071G>A synonymous_variant 0.15
rpsA 1834618 c.1077G>T synonymous_variant 0.15
rpsA 1834633 c.1092A>G synonymous_variant 0.16
rpsA 1834639 c.1098T>C synonymous_variant 0.16
rpsA 1834654 c.1113G>A synonymous_variant 0.15
rpsA 1834690 c.1149T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.88
thyA 3073892 c.580T>C synonymous_variant 0.12
thyA 3073917 c.555C>G synonymous_variant 0.14
thyA 3073925 c.547T>C synonymous_variant 0.13
thyA 3073929 c.543T>C synonymous_variant 0.14
thyA 3073953 c.519T>G synonymous_variant 0.17
thyA 3073958 c.514C>T synonymous_variant 0.14
thyA 3073959 c.513T>C synonymous_variant 0.15
thyA 3073977 c.495A>G synonymous_variant 0.15
thyA 3073989 c.483T>C synonymous_variant 0.16
thyA 3074001 c.471C>G synonymous_variant 0.13
thyA 3074004 c.468T>C synonymous_variant 0.12
thyA 3074010 c.462C>G synonymous_variant 0.13
thyA 3074120 c.352T>C synonymous_variant 0.14
thyA 3074121 c.351T>C synonymous_variant 0.13
thyA 3074127 c.345G>C synonymous_variant 0.13
thyA 3074130 c.342G>C synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.98
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877920 c.588G>C synonymous_variant 0.18
rpoA 3877926 c.582G>C synonymous_variant 0.19
rpoA 3877962 c.546G>T synonymous_variant 0.12
ddn 3986645 c.-199G>A upstream_gene_variant 0.13
ddn 3986648 c.-196C>G upstream_gene_variant 0.13
ddn 3986665 c.-179G>C upstream_gene_variant 0.13
ddn 3986667 c.-177_-176delCTinsAC upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.98
clpC1 4039298 c.1407T>C synonymous_variant 0.12
clpC1 4039577 c.1128T>C synonymous_variant 0.12
clpC1 4039610 c.1095G>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0