TB-Profiler result

Run: SRR11972445
Summary

Run ID: SRR11972445

Sample name:

Date: 03-04-2023 05:42:51

Number of reads: 861068

Percentage reads mapped: 79.8

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 0.95
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.97
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407695 p.Glu170* stop_gained 1.0 streptomycin
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
mshA 575851 c.504C>T synonymous_variant 1.0
rpoB 759940 p.Pro45Arg missense_variant 1.0
rpoC 763591 c.222C>A synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776381 c.2100C>T synonymous_variant 0.12
mmpL5 776384 c.2097C>A synonymous_variant 0.12
mmpL5 776387 c.2094T>C synonymous_variant 0.12
mmpL5 777344 p.Trp379Cys missense_variant 0.11
mmpL5 777591 p.Ser297* stop_gained 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416874 p.Phe158Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473620 n.-38C>A upstream_gene_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
inhA 1673826 c.-376C>A upstream_gene_variant 0.14
rpsA 1834588 c.1047C>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288814 p.Ala143Val missense_variant 0.88
pncA 2289862 c.-621C>A upstream_gene_variant 0.14
kasA 2518513 c.399C>A synonymous_variant 0.11
eis 2715069 c.264G>T synonymous_variant 0.11
folC 2747708 c.-110G>T upstream_gene_variant 0.17
Rv2752c 3065014 p.Val393Ala missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474670 p.Asp222Tyr missense_variant 0.11
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3641628 p.Ala32Ser missense_variant 0.12
rpoA 3877553 p.Glu319Lys missense_variant 1.0
embC 4240897 c.1035C>G synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245483 p.Gln751* stop_gained 0.18
embA 4246038 p.Ala936Ser missense_variant 0.12
embB 4246109 c.-405C>T upstream_gene_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269317 p.Ser173Ala missense_variant 0.55
ethA 4327130 p.Arg115Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407683 p.His174Asn missense_variant 0.11