TB-Profiler result

Run: ERR11050178
Summary

Run ID: ERR11050178

Sample name:

Date: 02-04-2023 14:56:09

Number of reads: 666099

Percentage reads mapped: 99.51

Strain: lineage4.1.2.1

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
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 1.0
lineage4.1.2.1 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
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 5771 p.Ala178Thr missense_variant 0.25
gyrB 6531 c.1293delC frameshift_variant 0.13
gyrA 7180 c.-122G>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8988 p.Thr563Pro missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491351 p.Asp190Val missense_variant 0.25
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576116 p.Ala257Pro missense_variant 0.67
mshA 576119 p.Ala258Pro missense_variant 0.25
mshA 576510 p.Thr388Ser missense_variant 0.33
mshA 576606 p.Ala420Gly missense_variant 0.25
mshA 576770 p.Arg475Ser missense_variant 1.0
ccsA 620051 p.Val54Gly missense_variant 0.4
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760867 p.Gly354Asp missense_variant 0.13
rpoB 761484 p.Gly560Arg missense_variant 0.17
rpoC 764374 c.1005C>T synonymous_variant 0.17
rpoC 764534 p.Arg389Gly missense_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765237 p.Asp623Ala missense_variant 0.15
rpoC 766974 p.Ala1202Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.4
mmpS5 778518 p.Gly130Ser missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303921 p.Ile331Phe missense_variant 0.18
fbiC 1305012 c.2082G>C synonymous_variant 0.2
Rv1258c 1407260 p.Ile27Met missense_variant 0.15
atpE 1461104 c.60C>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471793 n.-53G>T upstream_gene_variant 0.13
rrs 1472928 n.1083A>T non_coding_transcript_exon_variant 0.17
rrs 1473042 n.1197T>A non_coding_transcript_exon_variant 0.15
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.22
fabG1 1673553 p.Asp38Glu missense_variant 0.25
fabG1 1674065 p.Lys209Thr missense_variant 0.23
rpsA 1834415 p.Ala292Pro missense_variant 0.14
tlyA 1917833 c.-107G>T upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918286 p.Gly116Asp missense_variant 0.18
tlyA 1918621 p.Ser228Arg missense_variant 0.29
ndh 2101907 p.Val379Glu missense_variant 0.18
katG 2154437 p.Ala559Thr missense_variant 0.18
katG 2155261 p.Val284Gly missense_variant 0.25
katG 2155768 p.Ile115Asn missense_variant 0.22
katG 2155822 p.His97Pro missense_variant 0.14
katG 2155910 p.Val68Ile missense_variant 0.14
katG 2156376 c.-265C>T upstream_gene_variant 0.14
PPE35 2170035 p.Val193Gly missense_variant 0.4
PPE35 2170037 c.576C>G synonymous_variant 0.67
PPE35 2170082 c.531T>G synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2859933 c.486C>G synonymous_variant 0.25
ribD 2987048 c.210C>G synonymous_variant 0.15
thyX 3067480 p.Asp156Asn missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087653 c.834A>T synonymous_variant 0.15
fbiD 3339133 p.Asp6His missense_variant 0.2
fbiD 3339315 p.Glu66Asp missense_variant 0.25
Rv3083 3449069 p.Ala189Val missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474077 p.Lys24Thr missense_variant 0.18
fprA 3474430 p.Ser142Thr missense_variant 0.12
fprA 3475158 c.1152G>A synonymous_variant 0.11
whiB7 3568607 p.Pro25Ser missense_variant 0.14
whiB7 3568712 c.-33C>G upstream_gene_variant 1.0
Rv3236c 3612772 c.345T>C synonymous_variant 0.11
alr 3841485 c.-65G>C upstream_gene_variant 0.23
rpoA 3877799 p.Ser237Ala missense_variant 0.2
ddn 3986714 c.-130C>T upstream_gene_variant 0.12
ddn 3986868 p.Leu9Val missense_variant 0.21
clpC1 4039870 p.Arg279Cys missense_variant 1.0
clpC1 4040550 p.Leu52Trp missense_variant 0.2
panD 4043942 p.Pro114Ser missense_variant 0.25
embC 4242143 p.Pro761Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244030 c.798C>A synonymous_variant 0.9
embA 4245635 p.Lys801Asn missense_variant 0.27
embB 4246871 p.Ala120Thr missense_variant 0.12
embB 4247040 p.Phe176Cys missense_variant 0.29
embB 4249656 p.Val1048Ala missense_variant 0.11
aftB 4268619 p.Val73Gly missense_variant 0.35
aftB 4268623 p.Trp72Gly missense_variant 0.24
ethA 4326384 p.Thr364Pro missense_variant 0.11
ethR 4328030 p.Ala161Gly missense_variant 0.27
ethA 4328415 c.-942A>G upstream_gene_variant 0.27
whiB6 4338200 p.Asp108His missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407608 p.Pro199Ala missense_variant 0.14