TB-Profiler result

Run: ERR2652958
Summary

Run ID: ERR2652958

Sample name:

Date: 31-03-2023 22:25:11

Number of reads: 435359

Percentage reads mapped: 99.68

Strain: lineage4.4.1.1

Drug-resistance: HR-TB

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 0.98
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
katG 2155209 c.902delA frameshift_variant 0.12 isoniazid
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7691 c.390C>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575303 c.-45G>A upstream_gene_variant 0.13
mshA 575310 c.-38G>A upstream_gene_variant 0.13
rpoB 760820 p.Tyr338* stop_gained 0.18
rpoB 762718 p.Phe971Ser missense_variant 0.29
rpoB 762868 p.Tyr1021Cys missense_variant 1.0
rpoB 763102 p.Ala1099Glu missense_variant 0.14
rpoC 766144 c.2775G>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778243 c.237delC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801291 c.485delA frameshift_variant 0.13
fbiC 1302870 c.-61G>A upstream_gene_variant 0.13
rrs 1471653 n.-193C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472342 n.497G>A non_coding_transcript_exon_variant 0.14
rrl 1473423 n.-235C>T upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101826 p.Gly406Val missense_variant 0.12
ndh 2101864 p.Trp393* stop_gained 0.12
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169379 c.1233delG frameshift_variant 0.2
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170329 p.Ala95Val missense_variant 0.13
Rv1979c 2222889 c.276C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289749 c.-508G>A upstream_gene_variant 0.25
eis 2714729 p.Ala202Thr missense_variant 0.11
eis 2715213 c.120G>A synonymous_variant 0.12
folC 2746542 p.Ala353Thr missense_variant 0.18
Rv2752c 3065476 p.Ala239Val missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087698 c.879G>T synonymous_variant 0.14
ald 3087699 c.880C>T synonymous_variant 0.14
fbiD 3338970 c.-148C>G upstream_gene_variant 0.15
Rv3083 3448389 c.-114delA upstream_gene_variant 0.14
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474504 c.498G>A synonymous_variant 0.11
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3613309 c.-193G>T upstream_gene_variant 0.1
fbiB 3641373 c.-162C>T upstream_gene_variant 0.12
clpC1 4038972 p.Ile578Asn missense_variant 0.1
embC 4239665 c.-198G>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248132 p.Arg540His missense_variant 0.13
aftB 4267360 p.Met493Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0