TB-Profiler result

Run: SRR22528542

Summary

Run ID: SRR22528542

Sample name:

Date: 04-04-2023 04:18:23

Number of reads: 3090796

Percentage reads mapped: 99.74

Strain: lineage4.4.1.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.07
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 0.91
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage4.4.1 Euro-American (S-type) S;T None 0.91
lineage4.4.1.1 Euro-American S;Orphans None 0.9
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 0.95 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.88 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 8116 p.Thr272Ile missense_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.13
rpoB 761528 p.Asp574Glu missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
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
ndh 2102990 p.Val18Ala missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860144 p.Val92Gly missense_variant 0.13
thyA 3074495 c.-24C>T upstream_gene_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087828 p.Pro337Thr missense_variant 0.2
Rv3083 3448608 c.105G>A synonymous_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.17
whiB7 3568428 c.252A>G synonymous_variant 0.22
whiB7 3568437 c.243T>C synonymous_variant 0.17
whiB7 3568441 p.Lys80Thr missense_variant 0.11
Rv3236c 3612665 p.Val151Ala missense_variant 0.89
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
rpoA 3878637 c.-130G>C upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244970 c.1738C>T synonymous_variant 0.91
embB 4247028 p.Leu172Arg missense_variant 0.19
embB 4247033 p.Ser174Arg missense_variant 0.15
embB 4247039 p.Phe176Val missense_variant 0.17
embB 4247055 p.Leu181Gln missense_variant 0.18
embB 4248437 p.Thr642Ala missense_variant 0.85
ethR 4326703 c.-846T>C upstream_gene_variant 0.91
whiB6 4338514 p.Tyr3Cys missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.11