TB-Profiler result

Run: ERR2229592

Summary

Run ID: ERR2229592

Sample name:

Date: 31-03-2023 17:20:40

Number of reads: 587912

Percentage reads mapped: 99.09

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
gyrB 5965 c.726A>G synonymous_variant 0.17
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9571 p.Arg757Pro missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576579 p.Gly411Val missense_variant 0.2
rpoB 762517 p.Gly904Ala missense_variant 0.17
rpoB 763210 p.Asp1135Val missense_variant 0.18
rpoB 763283 p.Asn1159Lys missense_variant 0.18
rpoC 764448 c.1082delG frameshift_variant 0.2
rpoC 766136 c.2767C>A synonymous_variant 0.13
rpoC 766258 c.2889T>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775699 p.Ser928Ala missense_variant 0.17
mmpL5 777279 p.Ala401Val missense_variant 0.13
mmpL5 777287 c.1194G>A synonymous_variant 0.14
mmpS5 778887 p.Arg7Gly missense_variant 0.33
mmpR5 779326 p.Glu113Lys missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781695 p.Asn46His missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304849 p.Asn640Ile missense_variant 0.12
embR 1416877 c.471G>A synonymous_variant 0.17
embR 1417304 c.43delC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474117 n.460A>G non_coding_transcript_exon_variant 0.17
rrl 1475058 n.1401C>T non_coding_transcript_exon_variant 0.14
rrl 1476049 n.2394delG non_coding_transcript_exon_variant 0.18
rrl 1476278 n.2621G>A non_coding_transcript_exon_variant 0.4
fabG1 1674062 p.Ala208Val missense_variant 0.33
rpsA 1834255 c.714C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>T synonymous_variant 0.33
tlyA 1918632 c.693G>T synonymous_variant 0.14
ndh 2102604 c.439T>C synonymous_variant 0.5
ndh 2102610 c.433T>C synonymous_variant 0.5
katG 2153982 c.2130C>T synonymous_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.25
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169351 p.Ala421Asp missense_variant 0.22
PPE35 2169377 p.Phe412Leu missense_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.31
PPE35 2169910 p.Asn235Tyr missense_variant 0.27
PPE35 2170048 p.Leu189Val missense_variant 0.63
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170147 p.Ser156Ala missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290048 c.-809_-808dupGC upstream_gene_variant 0.17
kasA 2518045 c.-70G>A upstream_gene_variant 0.18
kasA 2518348 c.234A>T synonymous_variant 0.13
kasA 2518879 c.765A>G synonymous_variant 0.23
kasA 2518882 c.768C>A synonymous_variant 0.21
eis 2714139 c.1194C>A synonymous_variant 0.2
eis 2715544 c.-212G>T upstream_gene_variant 0.14
Rv2752c 3064578 c.1614C>T synonymous_variant 0.2
Rv2752c 3065300 p.Asp298Tyr missense_variant 0.29
thyX 3068011 c.-66C>T upstream_gene_variant 0.18
thyX 3068015 c.-70T>G upstream_gene_variant 0.18
fbiD 3339606 c.489G>A synonymous_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612049 c.1068G>T synonymous_variant 0.2
fbiB 3641605 p.Arg24Leu missense_variant 0.14
fbiB 3642047 c.513G>C synonymous_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.33
ddn 3986717 c.-127C>A upstream_gene_variant 0.14
clpC1 4038776 p.Glu643Asp missense_variant 0.13
clpC1 4039042 p.Ser555Thr missense_variant 0.14
clpC1 4039466 c.1239T>A synonymous_variant 0.2
clpC1 4039527 p.Arg393Gln missense_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.33
clpC1 4040088 c.615_616delTC frameshift_variant 0.25
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245128 c.1896G>T synonymous_variant 0.14
embA 4246050 p.Arg940Cys missense_variant 0.4
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 4246645 c.132G>A synonymous_variant 0.22
embB 4247025 p.Pro171Arg missense_variant 0.2
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4248307 c.1794G>T synonymous_variant 0.13
embB 4248779 p.Glu756Gln missense_variant 0.29
embB 4249601 p.Asp1030Asn missense_variant 0.2
ubiA 4269880 c.-47A>G upstream_gene_variant 0.18
ethA 4326400 c.1074A>T synonymous_variant 0.29
ethR 4326961 c.-588G>C upstream_gene_variant 0.25
ethR 4326964 c.-585G>A upstream_gene_variant 0.25
ethR 4326970 c.-579G>T upstream_gene_variant 0.25
ethA 4327100 p.Thr125Lys 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