TB-Profiler result

Run: SRR11972266
Summary

Run ID: SRR11972266

Sample name:

Date: 03-04-2023 05:34:10

Number of reads: 370351

Percentage reads mapped: 99.51

Strain: lineage2.2.1

Drug-resistance: RR-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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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 8485 p.Val395Ala missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576503 c.1158delC frameshift_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761379 p.Leu525Val missense_variant 0.33
rpoB 761530 p.Val575Gly missense_variant 0.12
rpoB 761674 p.Gly623Glu missense_variant 0.12
rpoB 762516 p.Gly904Ser missense_variant 0.12
rpoB 762536 p.Ile910Met missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763220 c.-150G>C upstream_gene_variant 0.13
rpoC 766342 c.2973C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775692 p.Ala930Val missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776507 c.1974C>G synonymous_variant 0.13
mmpL5 776976 p.Ser502Asn missense_variant 0.15
mmpL5 777951 p.Ala177Val missense_variant 0.12
mmpR5 779159 p.Ala57Val missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305322 p.Val798Leu missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461105 p.Ala21Thr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674026 p.Glu196Gly missense_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 0.95
rpsA 1834917 p.Thr459Ile missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918628 p.Leu230Pro missense_variant 0.17
ndh 2102073 p.Ala324Ser missense_variant 0.12
katG 2153909 p.Asp735His missense_variant 0.17
katG 2153972 p.Asp714Asn missense_variant 0.14
katG 2153988 c.2124C>T synonymous_variant 0.14
katG 2154210 c.1902C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155603 p.Asn170Ser missense_variant 0.29
katG 2155607 p.Gly169Ser missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168249 c.2364G>A synonymous_variant 0.17
PPE35 2168327 c.2286G>A synonymous_variant 0.14
Rv1979c 2222117 p.Met350Leu missense_variant 0.17
Rv1979c 2223147 c.18G>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289897 c.-656G>A upstream_gene_variant 0.22
pncA 2290214 c.-973T>C upstream_gene_variant 0.14
kasA 2518018 c.-97A>G upstream_gene_variant 0.25
kasA 2518406 p.Ala98Thr missense_variant 0.13
eis 2715042 c.291G>A synonymous_variant 0.12
eis 2715066 c.267G>A synonymous_variant 0.12
ahpC 2726447 c.255T>G synonymous_variant 0.15
Rv2752c 3064689 c.1503C>T synonymous_variant 1.0
Rv2752c 3065169 c.1023C>A synonymous_variant 0.2
Rv2752c 3065694 c.498G>A synonymous_variant 0.13
Rv2752c 3065970 c.222C>T synonymous_variant 0.18
thyX 3067966 c.-21G>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087067 p.Gly83Asp missense_variant 0.17
ald 3087116 c.297G>T synonymous_variant 0.13
Rv3083 3448404 c.-100C>T upstream_gene_variant 0.15
Rv3083 3449668 p.Gly389Cys missense_variant 0.17
fprA 3473986 c.-21G>A upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474719 p.Ala238Glu missense_variant 0.12
Rv3236c 3612760 c.357C>A synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641255 p.Ala238Val missense_variant 0.33
fbiB 3642312 p.Arg260Cys missense_variant 0.22
ddn 3986765 c.-79T>C upstream_gene_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.14
embC 4240759 c.897C>T synonymous_variant 0.15
embC 4242144 p.Pro761Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245124 p.Gly631Glu missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.85
ethR 4328128 p.Val194Met missense_variant 0.18
whiB6 4338473 p.Arg17Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407644 p.Arg187Trp missense_variant 0.13
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408059 p.His48Gln missense_variant 0.12