TB-Profiler result

Run: ERR2229638
Summary

Run ID: ERR2229638

Sample name:

Date: 31-03-2023 17:22:53

Number of reads: 602307

Percentage reads mapped: 99.12

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 6966 p.Ser576Asn missense_variant 0.12
gyrB 7085 p.Met616Val missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9456 p.Glu719Gln missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576488 p.Val381His missense_variant 0.29
ccsA 619761 c.-130G>A upstream_gene_variant 0.22
rpoB 760596 p.Thr264Ala missense_variant 0.15
rpoC 763680 p.Ile104Thr missense_variant 0.17
rpoC 764086 p.Asn239Lys missense_variant 0.22
rpoC 765038 c.1673delT frameshift_variant 0.33
rpoC 765539 p.Ala724Ser missense_variant 0.15
rpoC 766161 p.Asp931Val missense_variant 0.11
rpoC 766218 p.Asp950Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777176 p.Glu435Asp missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406210 p.His377Gln missense_variant 0.67
Rv1258c 1406909 c.432C>T synonymous_variant 0.29
embR 1416737 p.Arg204Gln missense_variant 0.17
embR 1416761 p.Ala196Asp missense_variant 0.25
embR 1417092 c.248_255delTCGGTGGC frameshift_variant 0.14
embR 1417102 c.246C>T synonymous_variant 0.14
embR 1417109 p.Arg80Leu missense_variant 0.14
embR 1417530 c.-183T>C upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474679 n.1022G>A non_coding_transcript_exon_variant 0.17
inhA 1674579 c.378G>C synonymous_variant 0.13
rpsA 1834602 p.Glu354Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102992 c.51T>G synonymous_variant 0.4
katG 2153926 p.Asp729Gly missense_variant 0.18
katG 2155537 p.Glu192Gly missense_variant 0.25
katG 2155982 p.Asn44Asp missense_variant 0.15
katG 2156115 c.-4T>C upstream_gene_variant 0.12
PPE35 2167973 c.2640A>G synonymous_variant 0.2
PPE35 2168231 c.2382T>A synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.19
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.29
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170157 p.Ala152Ser missense_variant 0.17
PPE35 2170220 c.393C>G synonymous_variant 0.18
Rv1979c 2223204 c.-40T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-124G>T upstream_gene_variant 0.17
pncA 2289626 c.-385G>A upstream_gene_variant 0.18
kasA 2518244 p.His44Asp missense_variant 0.17
kasA 2518809 p.Lys232Arg missense_variant 0.2
eis 2715030 c.303C>T synonymous_variant 0.15
eis 2715279 c.54A>G synonymous_variant 0.25
ahpC 2726724 p.Trp178Arg missense_variant 0.14
folC 2746148 p.Arg484Pro missense_variant 0.17
pepQ 2859656 p.Glu255* stop_gained 0.18
ribD 2986854 p.Gln6* stop_gained 0.2
Rv2752c 3065333 p.Ile287Phe missense_variant 0.25
Rv2752c 3067004 c.-813C>T upstream_gene_variant 0.13
ald 3087932 c.1113C>T synonymous_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.67
fbiB 3642121 p.Asp196Val missense_variant 0.15
alr 3840407 c.1014G>T synonymous_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.42
clpC1 4038314 c.2390delG frameshift_variant 0.18
clpC1 4038373 p.Gln778* stop_gained 0.2
clpC1 4038776 p.Glu643Asp missense_variant 0.12
clpC1 4040139 p.Pro189Leu missense_variant 0.17
clpC1 4040600 p.Leu35Phe missense_variant 0.14
panD 4044394 c.-113C>A upstream_gene_variant 0.2
embC 4240540 c.678C>A synonymous_variant 0.18
embC 4242078 p.Ser739Tyr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245590 c.-924G>A upstream_gene_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.23
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.88
embB 4246556 p.Ala15Pro missense_variant 0.88
embB 4246567 c.54_55insT frameshift_variant 0.5
embB 4248514 c.2001A>T synonymous_variant 0.17
embB 4249582 c.3069G>A synonymous_variant 0.67
aftB 4268744 c.93A>G synonymous_variant 0.12
ethA 4326355 p.Met373Ile missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0