TB-Profiler result

Run: SRR22528528
Summary

Run ID: SRR22528528

Sample name:

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

Number of reads: 1853841

Percentage reads mapped: 99.76

Strain: lineage4.4.1.1

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 0.96
lineage4.4 Euro-American S;T None 0.91
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.11
lineage4.4.1 Euro-American (S-type) S;T None 0.87
lineage4.4.1.1 Euro-American S;Orphans None 0.89
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 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.89 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
gyrB 6289 c.1050C>A synonymous_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8116 p.Thr272Ile missense_variant 0.8
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.12
rpoB 761528 p.Asp574Glu missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
rpoC 764546 p.Gly393Arg missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2
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 0.96
PPE35 2169840 p.Gly258Asp missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860144 p.Val92Gly missense_variant 0.17
pepQ 2860153 p.Glu89Ala missense_variant 0.12
thyA 3074495 c.-24C>T upstream_gene_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087828 p.Pro337Thr missense_variant 0.18
fbiD 3339726 c.609A>T synonymous_variant 0.16
Rv3083 3448608 c.105G>A synonymous_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.12
whiB7 3568428 c.252A>G synonymous_variant 0.15
whiB7 3568441 p.Lys80Thr missense_variant 0.16
Rv3236c 3612665 p.Val151Ala missense_variant 0.86
rpoA 3878648 c.-141C>G upstream_gene_variant 0.15
rpoA 3878662 c.-155G>T upstream_gene_variant 0.17
clpC1 4040902 c.-198T>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244970 c.1738C>T synonymous_variant 0.92
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4247039 p.Phe176Val missense_variant 0.11
embB 4248309 p.Phe599Cys missense_variant 0.12
embB 4248319 c.1806A>T synonymous_variant 0.18
embB 4248437 p.Thr642Ala missense_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.14
ethA 4326676 p.Ser266Arg missense_variant 0.12
ethR 4326703 c.-846T>C upstream_gene_variant 0.93
whiB6 4338514 p.Tyr3Cys missense_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.19