TB-Profiler result

Run: SRR6257040
Summary

Run ID: SRR6257040

Sample name:

Date: 04-04-2023 13:24:10

Number of reads: 2180946

Percentage reads mapped: 98.48

Strain: 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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 9034 p.Arg578Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575860 c.513G>A synonymous_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576113 c.766C>A synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762348 p.Ser848Pro missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766110 p.Pro914Leu missense_variant 0.15
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779597 c.-693delA upstream_gene_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>T upstream_gene_variant 0.11
fbiC 1304131 p.Ala401Thr missense_variant 0.14
Rv1258c 1406626 p.Tyr239His missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416222 p.Phe376Leu missense_variant 0.11
embR 1416232 p.Cys372Gly missense_variant 0.12
atpE 1461165 c.121C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
inhA 1673793 c.-409G>T upstream_gene_variant 0.17
inhA 1674099 c.-103G>T upstream_gene_variant 0.12
inhA 1674297 p.Gln32His missense_variant 0.17
inhA 1674911 p.Pro237Gln missense_variant 0.17
rpsA 1833876 p.Ala112Asp missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917802 c.-138T>C upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2169717 p.Asn299Ile missense_variant 0.12
PPE35 2169719 c.894C>T synonymous_variant 0.11
PPE35 2169840 p.Gly258Val missense_variant 0.11
PPE35 2170415 c.198A>C synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518529 p.Pro139Thr missense_variant 0.12
eis 2714476 p.Arg286His missense_variant 0.12
eis 2715062 p.His91Tyr missense_variant 0.15
eis 2715146 p.Leu63Met missense_variant 0.11
eis 2715462 c.-130G>T upstream_gene_variant 0.12
folC 2746959 p.Gly214Arg missense_variant 0.2
folC 2747159 p.Pro147Gln missense_variant 0.11
folC 2747179 c.420T>C synonymous_variant 0.11
pepQ 2859532 p.His296Arg missense_variant 0.12
pepQ 2859621 c.798G>T synonymous_variant 0.14
Rv2752c 3064580 p.Gly538Cys missense_variant 0.14
thyA 3073772 p.Asp234Tyr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087081 p.Gly88Trp missense_variant 0.14
ald 3087789 p.Leu324Ile missense_variant 0.12
fbiD 3339094 c.-24G>C upstream_gene_variant 0.11
fbiD 3339561 c.444C>A synonymous_variant 0.12
fbiD 3339595 p.Pro160Thr missense_variant 0.12
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.12
fprA 3474452 p.Arg149Gln missense_variant 0.12
fprA 3474747 p.Gln247His missense_variant 0.11
fprA 3475128 c.1122C>T synonymous_variant 0.12
fprA 3475258 p.Val418Phe missense_variant 0.1
Rv3236c 3612052 c.1065C>A synonymous_variant 0.2
Rv3236c 3612192 p.Gly309Trp missense_variant 0.2
Rv3236c 3612444 p.Ile225Val missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641820 p.Glu96* stop_gained 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.12
rpoA 3878626 c.-119A>G upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
embC 4240019 p.Asn53Asp missense_variant 0.15
embC 4240765 c.903C>A synonymous_variant 0.17
embC 4240843 c.981C>T synonymous_variant 0.12
embC 4240847 p.Asp329Asn missense_variant 0.12
embC 4242444 p.Pro861Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243065 p.Pro1068His missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245066 p.Phe612Leu missense_variant 0.15
embB 4245524 c.-990G>T upstream_gene_variant 0.15
embA 4245790 p.Thr853Asn missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246697 p.Gly62Trp missense_variant 0.12
embB 4247485 c.972C>A synonymous_variant 0.1
embB 4247594 p.Cys361Gly missense_variant 0.22
embB 4249411 c.2898G>A synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268414 c.423C>T synonymous_variant 0.12
aftB 4268825 c.12C>A synonymous_variant 0.11
ethR 4328044 p.Leu166Met missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407642 p.Arg187Ser missense_variant 0.15
gid 4407814 p.Gly130Asp missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408436 c.-234C>A upstream_gene_variant 0.17