TB-Profiler result

Run: ERR2229601
Summary

Run ID: ERR2229601

Sample name:

Date: 31-03-2023 17:20:59

Number of reads: 1085773

Percentage reads mapped: 99.24

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 7362 p.Glu21Gln missense_variant 0.97
fgd1 491339 p.Gly186Val missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576687 p.Glu447Gly missense_variant 0.11
ccsA 619940 p.Ala17Val missense_variant 0.14
rpoC 764341 c.972G>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776062 p.Thr807Ser missense_variant 0.17
mmpL5 776150 p.Met777Ile missense_variant 0.14
mmpL5 776173 p.Asp770Asn missense_variant 0.12
mmpL5 777781 p.Thr234Ala missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303564 p.Gly212Ser missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304337 c.1407C>A synonymous_variant 0.11
atpE 1460852 c.-192delT upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674759 c.558G>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154047 p.Trp689Arg missense_variant 0.18
katG 2154947 p.Ile389Val missense_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.28
PPE35 2167967 c.2646A>C synonymous_variant 0.28
PPE35 2167973 c.2640A>G synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289721 c.-480C>A upstream_gene_variant 0.12
folC 2746552 c.1047C>T synonymous_variant 0.13
Rv2752c 3065425 p.Gly256Asp missense_variant 0.25
thyX 3067444 p.Arg168Cys missense_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474860 p.Glu285Val missense_variant 0.15
Rv3236c 3612080 p.Ala346Asp missense_variant 0.13
fbiB 3641931 p.Arg133Ser missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.28
clpC1 4039022 c.1683A>G synonymous_variant 0.15
clpC1 4039486 p.Gly407Cys missense_variant 0.12
clpC1 4039546 p.Asp387Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243250 c.18T>C synonymous_variant 0.11
embA 4245586 p.Pro785Leu missense_variant 0.14
embB 4246034 c.-480G>T upstream_gene_variant 0.12
ubiA 4269137 p.Tyr233His missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0