TB-Profiler result

Run: ERR7910851
Summary

Run ID: ERR7910851

Sample name:

Date: 02-04-2023 06:32:05

Number of reads: 827175

Percentage reads mapped: 99.49

Strain: lineage4.1.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.97 para-aminosalicylic_acid
thyA 3073852 p.His207Arg missense_variant 1.0 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala 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 6613 c.-689A>T upstream_gene_variant 0.33
gyrB 7226 p.Ile663Phe missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490888 p.Thr36Pro missense_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576699 p.Glu451Ala missense_variant 0.27
rpoB 760012 p.Ala69Asp missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 763023 p.Tyr1073Asp missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765569 p.Ala734Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779076 c.-596G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.21
rrl 1474374 n.717T>G non_coding_transcript_exon_variant 0.13
rrl 1475572 n.1915T>A non_coding_transcript_exon_variant 0.3
fabG1 1673962 p.Asn175Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 0.96
ndh 2103013 p.Gln10His missense_variant 0.12
katG 2155853 p.Ser87Pro missense_variant 0.17
PPE35 2170066 p.Ala183Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288763 p.Thr160Lys missense_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2747342 p.Val86Gly missense_variant 0.16
Rv2752c 3066014 c.177dupG frameshift_variant 1.0
thyX 3067325 p.Glu207Asp missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339686 p.Asp190Ala missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612846 p.Pro91Ser missense_variant 1.0
Rv3236c 3612974 p.Ile48Ser missense_variant 0.22
alr 3840486 p.Ile312Ser missense_variant 0.19
alr 3840495 p.Leu309Arg missense_variant 0.14
rpoA 3878344 p.Arg55Leu missense_variant 0.29
clpC1 4040409 p.Gly99Phe missense_variant 0.18
embC 4241679 p.Val606Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244880 p.Trp550Gly missense_variant 0.18
embA 4245210 c.1978C>T synonymous_variant 0.17
embB 4249082 p.Thr857Ala missense_variant 0.14
aftB 4267713 p.Leu375Arg missense_variant 0.25
aftB 4267911 p.Pro309Leu missense_variant 0.18
aftB 4268253 p.Leu195Arg missense_variant 0.23
ubiA 4269205 p.Leu210Pro missense_variant 0.13
ubiA 4269721 p.Ala38Val missense_variant 1.0
ethA 4327325 p.Tyr50Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338708 c.-188delG upstream_gene_variant 0.25
gid 4407916 p.Arg96Leu missense_variant 0.95