TB-Profiler result

Run: ERR2229674
Summary

Run ID: ERR2229674

Sample name:

Date: 31-03-2023 17:24:41

Number of reads: 549445

Percentage reads mapped: 99.19

Strain: lineage4.8

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
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
ethA 4327292 p.Thr61Met missense_variant 0.22 ethionamide
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 1.0
gyrA 8471 c.1170T>C synonymous_variant 0.11
fgd1 491071 p.Tyr97Asn missense_variant 0.17
fgd1 491501 p.Glu240Gly missense_variant 0.12
fgd1 491521 c.739C>A synonymous_variant 0.12
fgd1 491574 p.Asp264Glu missense_variant 0.12
rpoB 759611 c.-196G>T upstream_gene_variant 0.4
rpoC 764210 p.Ile281Val missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776307 p.Asp725Gly missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407020 c.321C>A synonymous_variant 0.12
embR 1417090 c.258C>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102818 c.225G>A synonymous_variant 0.4
PPE35 2167965 p.Ala883Gly missense_variant 0.4
PPE35 2167967 c.2646A>C synonymous_variant 0.4
PPE35 2168621 c.1992C>T synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169091 p.Val508Leu missense_variant 0.33
PPE35 2169095 p.Leu506Phe missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519337 p.Asn408Ile missense_variant 0.17
pepQ 2860579 c.-161A>C upstream_gene_variant 0.17
ald 3087158 c.339G>A synonymous_variant 0.15
ald 3087195 p.Ala126Thr missense_variant 0.12
ald 3087872 c.1053G>T synonymous_variant 0.12
whiB7 3568505 c.175C>A synonymous_variant 0.15
alr 3840504 p.Asn306Ile missense_variant 0.29
rpoA 3878622 c.-115C>A upstream_gene_variant 1.0
clpC1 4040605 p.Leu34Val missense_variant 0.14
panD 4044003 p.Met93Ile missense_variant 0.25
panD 4044083 p.Gly67Cys missense_variant 0.29
panD 4044313 c.-32C>T upstream_gene_variant 0.22
panD 4044438 c.-157G>T upstream_gene_variant 0.15
embC 4239837 c.-26A>G upstream_gene_variant 0.13
embC 4241811 p.Trp650Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4248833 p.Trp774Gly missense_variant 0.2
ubiA 4269777 p.Lys19Asn missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407552 c.651G>T synonymous_variant 0.17
gid 4407626 p.Ala193Ser missense_variant 0.17
gid 4407891 p.Met104Ile missense_variant 0.47
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0