TB-Profiler result

Run: ERR11050817
Summary

Run ID: ERR11050817

Sample name:

Date: 03-04-2023 22:21:11

Number of reads: 2923577

Percentage reads mapped: 99.59

Strain: lineage4.7;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 0.36
lineage4.7 Euro-American (mainly T) T1;T5 None 0.63
lineage4.1.2 Euro-American T;H None 0.37
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.35
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 7270 c.-32C>T upstream_gene_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.28
gyrA 9304 p.Gly668Asp missense_variant 0.39
fgd1 491591 p.Lys270Met missense_variant 0.28
mshA 575679 p.Asn111Ser missense_variant 0.41
mshA 576442 p.Cys365Trp missense_variant 0.21
mshA 576456 p.Val370Gly missense_variant 0.17
mshA 576458 p.Ala371Thr missense_variant 0.11
mshA 576468 p.Val374Gly missense_variant 0.24
mshA 576616 c.1269G>C synonymous_variant 0.2
rpoB 759852 p.Ser16Cys missense_variant 0.3
rpoB 760115 c.309C>T synonymous_variant 0.29
rpoC 764367 p.Gly333Ala missense_variant 0.26
rpoC 765150 p.Gly594Glu missense_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777824 p.Leu219Phe missense_variant 0.38
mmpL5 777883 p.Gly200Arg missense_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.66
fabG1 1673553 p.Asp38Glu missense_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168151 p.Thr821Asn missense_variant 0.62
PPE35 2170675 c.-63G>C upstream_gene_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290016 c.-775T>C upstream_gene_variant 0.61
kasA 2518076 c.-39C>T upstream_gene_variant 0.41
kasA 2518573 c.459G>T synonymous_variant 0.59
kasA 2519071 p.Asp319Glu missense_variant 0.27
pepQ 2860159 p.Ala87Gly missense_variant 0.12
thyX 3067944 p.Val1Gly missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.32
ald 3087816 p.Cys333Gly missense_variant 0.24
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fbiD 3339751 p.Ala212Pro missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.31
rpoA 3878613 c.-106A>C upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.5
embC 4240409 p.Pro183Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
embB 4246527 p.Ala5Gly missense_variant 0.47
embB 4247016 p.Ser168Trp missense_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.31
embB 4249732 c.3219C>G synonymous_variant 0.54
aftB 4267981 p.Arg286Gly missense_variant 0.28
ethA 4328415 c.-942A>G upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0