TB-Profiler result

Run: ERR2228999
Summary

Run ID: ERR2228999

Sample name:

Date: 31-03-2023 16:29:54

Number of reads: 322084

Percentage reads mapped: 99.53

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 5916 p.Val226Asp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 619844 c.-46delC upstream_gene_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775882 p.Asn867Tyr missense_variant 0.2
mmpL5 777119 p.His454Gln missense_variant 0.33
mmpL5 777122 c.1359C>T synonymous_variant 0.33
mmpL5 777128 c.1353A>G synonymous_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781538 c.-21delC upstream_gene_variant 0.33
fbiC 1302785 c.-146A>G upstream_gene_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472116 n.271C>G non_coding_transcript_exon_variant 0.22
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1473350 n.1505T>C non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834589 p.Asp350Asn missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102907 p.Thr46Ser missense_variant 0.3
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2168014 p.Ala867Thr missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168958 p.Ala552Gly missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290096 c.-855C>G upstream_gene_variant 0.2
kasA 2518864 c.750G>C synonymous_variant 0.25
eis 2715297 p.Asp12Glu missense_variant 0.13
pepQ 2859949 p.Leu157* stop_gained 0.5
pepQ 2860574 c.-156C>T upstream_gene_variant 0.29
fprA 3474806 p.Met267Lys missense_variant 0.22
alr 3840888 p.Ala178Val missense_variant 0.14
rpoA 3877606 p.Leu301Arg missense_variant 0.2
clpC1 4039645 p.His354Asp missense_variant 0.27
clpC1 4039664 c.1041G>C synonymous_variant 0.15
clpC1 4039714 p.Tyr331His missense_variant 0.12
panD 4044156 c.126A>G synonymous_variant 0.22
embC 4239749 c.-114T>A upstream_gene_variant 0.25
embC 4241510 p.Met550Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244577 p.Thr449Ser missense_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
ubiA 4269631 p.Ala68Val missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethR 4326982 c.-567C>G upstream_gene_variant 0.2
ethA 4326990 p.Ile162Phe missense_variant 0.25
ethA 4328412 c.-939G>C upstream_gene_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