TB-Profiler result

Run: ERR2229724
Summary

Run ID: ERR2229724

Sample name:

Date: 31-03-2023 17:29:17

Number of reads: 758930

Percentage reads mapped: 99.18

Strain: lineage4

Drug-resistance: Other

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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
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
thyA 3074223 p.Trp83* stop_gained 0.12 para-aminosalicylic_acid
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 6126 p.Gly296Val missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 766136 p.Arg923Trp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304224 p.Gly432Cys missense_variant 0.12
Rv1258c 1406966 p.Asp125Glu missense_variant 0.14
embR 1417375 c.-28T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476468 n.2811C>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
rpsA 1833784 c.243C>A synonymous_variant 0.18
rpsA 1834368 p.Leu276Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103048 c.-6C>A upstream_gene_variant 0.22
katG 2155350 c.762C>T synonymous_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169366 p.Ser416Asn missense_variant 0.14
PPE35 2169725 c.888T>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.37
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289754 c.-513G>A upstream_gene_variant 0.22
pncA 2289766 c.-525T>C upstream_gene_variant 0.2
pncA 2289964 c.-723C>A upstream_gene_variant 0.14
eis 2715038 c.268_294delACGCATCGCCGGCGCGGCTTGCTGCGC conservative_inframe_deletion 0.25
folC 2747245 c.354G>T synonymous_variant 0.17
ribD 2987518 p.Ile227Thr missense_variant 0.12
Rv2752c 3065883 c.309C>T synonymous_variant 0.12
ald 3087730 p.Ser304Leu missense_variant 0.15
fprA 3474165 c.159C>G synonymous_variant 0.11
clpC1 4038241 p.Gly822Cys missense_variant 0.13
clpC1 4038740 c.1965G>C synonymous_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.18
embC 4240712 p.Trp284Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244854 p.Val541Ala missense_variant 1.0
embA 4244858 c.1626G>T synonymous_variant 1.0
embA 4244861 c.1629G>C synonymous_variant 1.0
embA 4244863 p.Leu544Gln missense_variant 1.0
embA 4244865 p.Ala545Pro missense_variant 1.0
embA 4244868 p.Ser546Arg missense_variant 1.0
embA 4244871 p.Gly547His missense_variant 1.0
embA 4245103 p.Trp624Leu missense_variant 0.12
aftB 4267220 c.1617C>A synonymous_variant 0.12
aftB 4267986 p.Arg284His missense_variant 0.17
aftB 4268774 p.Ser21Arg missense_variant 0.18
aftB 4269027 c.-191C>A upstream_gene_variant 0.18
ethA 4327142 p.Thr111Asn missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0