TB-Profiler result

Run: SRR1174307
Summary

Run ID: SRR1174307

Sample name:

Date: 03-04-2023 03:34:47

Number of reads: 5523337

Percentage reads mapped: 98.87

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 1.0
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761131 p.Gly442Glu missense_variant 0.12 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.3 isoniazid, ethionamide
inhA 1674048 c.-154G>A upstream_gene_variant 0.25 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289222 p.Val7Gly missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326707 p.Trp256* stop_gained 1.0 ethionamide
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 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8366 c.1065G>A synonymous_variant 0.2
gyrA 8990 c.1689C>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490936 p.Pro52Thr missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.97
mshA 575644 c.297G>T synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620100 c.210G>A synonymous_variant 0.14
ccsA 620465 p.Ala192Val missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761366 c.1560C>T synonymous_variant 0.12
rpoC 762977 c.-393C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765198 p.Gly610Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777319 p.Arg388Gly missense_variant 0.2
mmpL5 777748 p.Gly245Trp missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407122 c.219G>A synonymous_variant 0.14
embR 1417262 p.Pro29Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674424 c.225delC frameshift_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155431 c.681G>A synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518415 p.Pro101Ser missense_variant 0.13
eis 2714710 p.Pro208His missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642194 c.660C>T synonymous_variant 0.15
embC 4242642 p.Arg927His missense_variant 0.13
embA 4243346 c.114A>G synonymous_variant 0.98
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243699 p.Pro156Leu missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0