TB-Profiler result

Run: ERR2229113
Summary

Run ID: ERR2229113

Sample name:

Date: 31-03-2023 16:40:03

Number of reads: 443014

Percentage reads mapped: 99.42

Strain: lineage4.8

Drug-resistance: HR-TB

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155345 c.766delG frameshift_variant 0.17 isoniazid
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 8786 c.1485T>C synonymous_variant 0.15
fgd1 491034 c.252C>A synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.36
mshA 576111 p.Ala255Gly missense_variant 0.29
rpoC 767124 p.Val1252Glu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.14
mmpL5 777164 c.1317C>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800862 c.54C>T synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471915 n.70C>A non_coding_transcript_exon_variant 0.15
rrl 1473552 n.-106G>T upstream_gene_variant 0.5
rrl 1475476 n.1819G>A non_coding_transcript_exon_variant 0.25
rrl 1476274 n.2617G>T non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
inhA 1674691 p.Ala164Thr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154582 c.1530C>T synonymous_variant 0.2
katG 2154877 p.Trp412Leu missense_variant 0.29
katG 2155204 p.Ser303* stop_gained 0.29
PPE35 2167965 c.2646_2647delAG frameshift_variant 0.33
PPE35 2167973 c.2640A>G synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169732 p.Asn294Ser missense_variant 0.12
PPE35 2169749 c.864A>T synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170528 p.Ser29Ala missense_variant 0.15
PPE35 2170529 c.84G>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.17
pepQ 2860026 c.393G>A synonymous_variant 0.18
Rv2752c 3065275 p.Gly306Ala missense_variant 0.22
Rv2752c 3065519 p.Leu225Ile missense_variant 0.15
ald 3086680 c.-139delT upstream_gene_variant 0.22
Rv3236c 3612107 c.1009delT frameshift_variant 0.15
Rv3236c 3612277 c.840G>A synonymous_variant 0.17
clpC1 4038835 p.Phe624Ile missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244693 c.1461C>T synonymous_variant 0.22
embB 4246187 c.-327C>T upstream_gene_variant 0.2
embB 4246894 c.381C>T synonymous_variant 0.2
embB 4247512 c.999T>C synonymous_variant 0.29
embB 4247516 p.Asn335Asp missense_variant 0.29
embB 4249532 p.Ala1007Thr missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1418del transcript_ablation 1.0