TB-Profiler result

Run: ERR4972579
Summary

Run ID: ERR4972579

Sample name:

Date: 01-04-2023 21:47:58

Number of reads: 952558

Percentage reads mapped: 99.19

Strain: lineage4.1.2.1.1

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 1.0
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) T1;H1 RD182 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 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407872 c.329_330delTG frameshift_variant 1.0 streptomycin
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575252 c.-96C>T upstream_gene_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576079 c.732G>A synonymous_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760899 p.Asp365Asn missense_variant 0.25
rpoB 761035 p.Thr410Met missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765860 p.Phe831Ile missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777262 p.Thr407Ser missense_variant 0.2
mmpL5 777793 p.Ala230Thr missense_variant 1.0
mmpL5 777947 c.534G>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801147 c.339T>C synonymous_variant 0.11
rplC 801185 p.Thr126Ile missense_variant 0.14
Rv1258c 1407335 p.Arg2Ser missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673560 p.Lys41Leu missense_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169751 p.Gly288* stop_gained 1.0
PPE35 2169956 c.657T>C synonymous_variant 0.11
PPE35 2169964 p.Leu217Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289728 c.-487A>G upstream_gene_variant 0.14
pncA 2289733 c.-492G>T upstream_gene_variant 0.15
pncA 2289973 c.-732T>A upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519167 c.1053T>C synonymous_variant 0.25
kasA 2519171 p.Leu353Val missense_variant 0.25
pepQ 2859852 c.567A>G synonymous_variant 0.13
ribD 2986666 c.-173G>T upstream_gene_variant 0.15
ald 3086670 c.-150G>T upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087359 c.540C>A synonymous_variant 0.11
Rv3083 3449881 p.Trp460Arg missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474622 p.Ala206Ser missense_variant 0.17
whiB7 3568425 c.255T>G synonymous_variant 0.25
fbiB 3642204 p.Asp224Tyr missense_variant 0.22
fbiB 3642226 p.Gln231Pro missense_variant 0.25
fbiB 3642229 p.Leu232Gln missense_variant 0.29
fbiB 3642232 p.Leu233Gln missense_variant 0.29
fbiB 3642234 p.Arg234Leu missense_variant 0.29
rpoA 3877500 c.1008C>T synonymous_variant 0.29
rpoA 3877597 p.Leu304Gln missense_variant 0.12
clpC1 4039121 c.1584T>C synonymous_variant 0.2
clpC1 4039931 c.774T>A synonymous_variant 0.11
clpC1 4040241 p.Thr155Phe missense_variant 0.22
clpC1 4040249 p.Glu152Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268622 p.Trp72Leu missense_variant 0.18
aftB 4268988 c.-152G>A upstream_gene_variant 0.12
whiB6 4338418 p.Thr35Met missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0