TB-Profiler result

Run: SRR10868975
Summary

Run ID: SRR10868975

Sample name:

Date: 02-04-2023 19:34:19

Number of reads: 479959

Percentage reads mapped: 99.38

Strain: lineage4.1.1.3

Drug-resistance: MDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9570 p.Arg757Cys missense_variant 0.12
fgd1 491021 p.Arg80His missense_variant 0.12
mshA 575392 p.Gln15His missense_variant 0.12
mshA 576735 p.Leu463Pro missense_variant 0.14
rpoC 763931 p.Gly188Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765981 p.Gly871Asp missense_variant 0.11
rpoC 767104 c.3735C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777721 p.Arg254Trp missense_variant 0.17
mmpL5 778260 p.Ser74Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302775 c.-156C>A upstream_gene_variant 0.14
Rv1258c 1406985 p.Ala119Glu missense_variant 0.17
Rv1258c 1407269 c.72C>T synonymous_variant 0.12
embR 1417192 c.156C>T synonymous_variant 0.18
embR 1417248 c.99delC frameshift_variant 0.2
embR 1417257 p.Gly31Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475299 n.1642G>A non_coding_transcript_exon_variant 0.13
inhA 1673474 c.-728C>G upstream_gene_variant 1.0
inhA 1674283 p.Val28Ile missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918057 p.Val40Ile missense_variant 0.12
katG 2154181 p.Gly644Asp missense_variant 0.12
katG 2156255 c.-144T>C upstream_gene_variant 0.1
Rv1979c 2222835 c.330T>C synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290058 c.-817G>A upstream_gene_variant 0.12
ribD 2987378 c.540C>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840843 p.Leu193Pro missense_variant 0.11
embC 4241384 p.Pro508Thr missense_variant 0.11
embC 4241863 p.Glu667Asp missense_variant 0.17
embA 4242551 c.-682C>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246132 p.Leu967Pro missense_variant 0.11
embA 4246190 p.Asn986Lys missense_variant 0.12
embB 4249047 p.Ala845Val missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267865 c.972G>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0