TB-Profiler result

Run: SRR1172215
Summary

Run ID: SRR1172215

Sample name:

Date: 03-04-2023 02:59:35

Number of reads: 781518

Percentage reads mapped: 98.07

Strain: lineage4.1.1

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
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 761141 p.His445Gln missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288751 p.Ser164* stop_gained 0.11 pyrazinamide
pncA 2288953 p.Gly97Cys missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 6480 p.Ala414Glu missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763421 p.Glu18* stop_gained 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156453 c.-342C>A upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714873 p.Pro154Thr missense_variant 0.12
ahpC 2726210 c.18T>C synonymous_variant 1.0
folC 2746788 p.Ala271Ser missense_variant 0.14
pepQ 2860010 p.Ala137Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087726 p.Ala303Ser missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641183 p.Ser214Tyr missense_variant 0.11
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642621 p.Ala363Thr missense_variant 0.13
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.43
rpoA 3878601 c.-95delG upstream_gene_variant 0.36
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.27
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244657 c.1425G>T synonymous_variant 0.11
embA 4244750 c.1518C>A synonymous_variant 0.12
embB 4246660 c.147C>T synonymous_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269731 p.Ala35Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407756 p.Ser149Arg missense_variant 1.0