TB-Profiler result

Run: ERR2229593
Summary

Run ID: ERR2229593

Sample name:

Date: 31-03-2023 17:20:38

Number of reads: 945231

Percentage reads mapped: 99.16

Strain: lineage4.8

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
lineage4.8 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
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 6901 c.-401G>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8639 c.1338G>T synonymous_variant 0.11
gyrA 8776 p.Asp492Val missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576482 p.Val379Leu missense_variant 0.13
rpoB 759723 c.-84C>T upstream_gene_variant 0.13
rpoB 759726 c.-81A>T upstream_gene_variant 0.13
rpoB 759727 c.-80A>T upstream_gene_variant 0.12
rpoB 759730 c.-77A>G upstream_gene_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775908 p.Leu858Pro missense_variant 0.12
mmpL5 776384 c.2097C>T synonymous_variant 0.13
mmpL5 777164 c.1317C>T synonymous_variant 0.12
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.11
mmpS5 778630 p.Leu92Phe missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303400 p.Gln157Leu missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
tlyA 1917881 c.-59C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154614 p.Gln500* stop_gained 0.11
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2167967 c.2646A>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169879 p.Phe245Ser missense_variant 0.15
PPE35 2169882 p.Ser244Asn missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715060 p.His91Met missense_variant 0.11
eis 2715065 p.Thr90Ala missense_variant 0.11
ahpC 2725926 c.-267T>C upstream_gene_variant 0.11
pepQ 2859825 c.594C>A synonymous_variant 0.12
Rv2752c 3064674 c.1518C>A synonymous_variant 0.17
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.2
alr 3840736 p.Phe229Leu missense_variant 0.1
alr 3841546 c.-126C>A upstream_gene_variant 0.25
clpC1 4038634 p.Glu691Gln missense_variant 0.12
clpC1 4039835 c.870C>T synonymous_variant 0.12
clpC1 4040458 p.Arg83Gly missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244717 p.Trp495* stop_gained 0.12
embB 4246555 c.42G>C synonymous_variant 0.35
embB 4246556 p.Ala15Pro missense_variant 0.35
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4247470 c.957T>C synonymous_variant 0.13
embB 4247472 p.Phe320Tyr missense_variant 0.13
ethR 4327850 p.Asn101Ser missense_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