TB-Profiler result

Run: ERR2229179
Summary

Run ID: ERR2229179

Sample name:

Date: 31-03-2023 16:47:24

Number of reads: 835359

Percentage reads mapped: 99.41

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 2155193 p.Gly307Arg missense_variant 0.11 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 7349 p.Glu16Asp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491317 p.Pro179Ser missense_variant 0.14
mshA 576482 p.Val379Leu missense_variant 0.15
mshA 576721 c.1374G>A synonymous_variant 0.13
ccsA 620842 p.His318Tyr missense_variant 0.12
rpoC 767023 c.3654C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303037 p.Gly36Asp missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304243 p.Pro438Arg missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474713 n.1056T>C non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
inhA 1674500 p.Gln100Arg missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102482 c.561A>T synonymous_variant 0.14
ndh 2103236 c.-194C>T upstream_gene_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168140 p.Ala825Thr missense_variant 0.12
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.49
Rv1979c 2222576 p.Trp197Arg missense_variant 0.12
Rv1979c 2222979 c.186G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518758 p.Ala215Val missense_variant 0.15
eis 2715206 p.Asp43Asn missense_variant 0.12
eis 2715518 c.-186G>A upstream_gene_variant 0.13
ahpC 2725961 c.-232C>A upstream_gene_variant 0.15
thyA 3074410 p.Arg21His missense_variant 0.2
thyA 3074507 c.-36G>T upstream_gene_variant 0.22
alr 3841175 c.246G>T synonymous_variant 0.12
rpoA 3877895 p.Arg205Cys missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242692 p.Arg944Trp missense_variant 0.15
embA 4246426 p.Pro1065Leu missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4248332 p.Ala607Thr missense_variant 0.13
embB 4249453 c.2940G>A synonymous_variant 0.13
ethA 4328452 c.-979C>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0