TB-Profiler result

Run: SRR1003108
Summary

Run ID: SRR1003108

Sample name:

Date: 02-04-2023 14:24:01

Number of reads: 16230953

Percentage reads mapped: 98.61

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155977 c.133_134delCT frameshift_variant 0.38 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4324455 c.899_*1548del frameshift_variant&stop_lost&splice_region_variant 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9147 p.Pro621Gln missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 0.98
fgd1 491189 p.Val136Ala missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760600 p.Asp265Val missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 763874 p.Glu169Lys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpL5 777602 p.Gln293His missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
fbiC 1303007 p.Leu26* stop_gained 0.16
fbiC 1303147 p.Ala73Thr missense_variant 0.2
fbiC 1303151 p.Gly74Val missense_variant 0.22
fbiC 1303157 p.His76Leu missense_variant 0.21
fbiC 1303350 p.Cys140* stop_gained 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406853 p.Leu163Trp missense_variant 0.22
embR 1416715 c.633G>A synonymous_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473632 n.-26G>A upstream_gene_variant 1.0
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918070 p.Thr44Asn missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156105 p.Glu3* stop_gained 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2222303 p.Thr288Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288736 p.Val169Asp missense_variant 0.14
pncA 2289108 p.Val45Glu missense_variant 1.0
folC 2747081 p.Val173Asn missense_variant 0.12
folC 2747086 c.513A>G synonymous_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449000 p.Pro166Leu missense_variant 1.0
Rv3083 3449876 p.His458Arg missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840999 p.Leu141Pro missense_variant 0.1
alr 3841146 p.Ala92Asp missense_variant 1.0
embC 4240423 c.561G>A synonymous_variant 1.0
embC 4241632 p.Phe590Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244154 p.Thr308Ser missense_variant 0.12
embB 4246598 c.86delT frameshift_variant 0.13
embB 4249000 c.2488_2489delAC frameshift_variant 0.13
aftB 4267647 p.Asp397Gly 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 0.99