TB-Profiler result

Run: ERR2229723
Summary

Run ID: ERR2229723

Sample name:

Date: 31-03-2023 17:30:26

Number of reads: 1042438

Percentage reads mapped: 99.28

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 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 2154222 c.1889delG frameshift_variant 0.12 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
gyrB 6247 p.Lys336Asn missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576766 c.1419G>C synonymous_variant 0.25
mshA 576772 c.1425T>A synonymous_variant 0.2
rpoB 760317 p.Ser171Cys missense_variant 0.15
rpoC 763532 p.Thr55Ser missense_variant 0.17
rpoC 763702 c.333C>G synonymous_variant 0.11
rpoC 764508 p.Ala380Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776240 p.Lys747Asn missense_variant 0.12
mmpL5 776463 p.Ser673Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781504 c.-56G>T upstream_gene_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417454 c.-107C>A upstream_gene_variant 0.25
atpE 1461102 p.Gly20Cys missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472878 n.1033G>T non_coding_transcript_exon_variant 0.12
rrs 1472880 n.1035G>T non_coding_transcript_exon_variant 0.12
rrs 1473262 n.1417T>A non_coding_transcript_exon_variant 0.13
rrs 1473341 n.1496A>G non_coding_transcript_exon_variant 0.12
rrl 1473994 n.337C>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474250 n.593A>T non_coding_transcript_exon_variant 0.14
rrl 1476426 n.2769A>T non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.22
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673357 c.-83G>A upstream_gene_variant 0.16
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
rpsA 1833392 c.-150C>A upstream_gene_variant 0.17
rpsA 1834233 c.694delG frameshift_variant 0.18
rpsA 1834392 p.Trp284* stop_gained 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.17
katG 2154237 c.1875G>T synonymous_variant 0.12
katG 2154466 p.Cys549Phe missense_variant 0.12
PPE35 2167897 p.Asn906Asp missense_variant 0.1
PPE35 2167955 c.2658A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2167973 c.2640A>G synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169021 p.Gly531Val missense_variant 0.2
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170147 p.Ser156Ala missense_variant 0.19
Rv1979c 2222614 p.Ile184Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223331 c.-167C>A upstream_gene_variant 0.13
pncA 2288944 p.Thr100Ala missense_variant 0.13
pncA 2289966 c.-725G>A upstream_gene_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.17
kasA 2518609 p.Met165Ile missense_variant 0.11
kasA 2519141 c.1027C>T synonymous_variant 0.17
kasA 2519302 p.Tyr396* stop_gained 0.14
folC 2746467 c.1131_1132insTCGTG frameshift_variant 0.13
folC 2746923 p.Gly226Cys missense_variant 0.17
fbiD 3339499 c.384_393delAATCTCGGCC frameshift_variant 0.12
Rv3083 3448427 c.-77C>A upstream_gene_variant 0.12
fbiA 3640481 c.-62G>T upstream_gene_variant 0.22
fbiA 3640492 c.-51G>T upstream_gene_variant 0.2
fbiA 3640513 c.-30G>T upstream_gene_variant 0.18
fbiA 3640521 c.-22C>A upstream_gene_variant 0.18
fbiA 3640565 p.Gly8Ala missense_variant 0.15
fbiB 3641656 p.Arg41Leu missense_variant 0.13
fbiB 3642756 p.Val408Phe missense_variant 0.14
alr 3840528 p.Thr298Lys missense_variant 0.13
rpoA 3877559 p.Pro317Thr missense_variant 0.15
clpC1 4040495 c.209delG frameshift_variant 0.14
panD 4044170 p.Leu38Met missense_variant 0.18
embC 4241075 p.Gly405Cys missense_variant 0.13
embC 4241847 p.Thr662Asn missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245559 p.Gly776Val missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.36
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246567 c.54_55insT frameshift_variant 0.27
embB 4247028 p.Leu172Arg missense_variant 0.18
ubiA 4269260 p.Arg192Ser missense_variant 0.13
ethA 4327563 c.-90C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0