TB-Profiler result

Run: SRR1180926
Summary

Run ID: SRR1180926

Sample name:

Date: 03-04-2023 04:17:13

Number of reads: 738478

Percentage reads mapped: 95.78

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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 5552 p.Ala105Pro missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7612 p.Ser104* stop_gained 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491493 c.711C>T synonymous_variant 0.12
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 761344 p.Val513Ala missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776133 p.Ala783Glu missense_variant 0.12
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 779280 c.-800G>A upstream_gene_variant 0.13
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 1407176 c.165G>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
inhA 1674708 p.Glu169Asp missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155112 p.Glu334Gln missense_variant 0.11
katG 2155155 c.957C>T synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288681 c.561A>G stop_lost&splice_region_variant 0.92
pncA 2288944 p.Thr100Pro missense_variant 1.0
kasA 2518367 c.253C>A synonymous_variant 0.15
folC 2746280 p.Ile440Thr missense_variant 0.2
ribD 2986852 p.Gly5Asp missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840803 c.618C>A synonymous_variant 0.13
rpoA 3877969 p.Ala180Val missense_variant 1.0
clpC1 4039521 p.Leu395Gln missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243228 c.-5G>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4246980 p.Gly156Asp missense_variant 0.11
aftB 4266967 p.Pro624Ser missense_variant 0.12
aftB 4266974 c.1863C>G synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268080 p.Gly253Ser missense_variant 0.22
ethA 4326648 p.Tyr276His 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