TB-Profiler result

Run: SRR6832272
Summary

Run ID: SRR6832272

Sample name:

Date: 04-04-2023 17:19:58

Number of reads: 656507

Percentage reads mapped: 99.48

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 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4327033 p.Tyr147* 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8565 p.Ile422Val missense_variant 0.2
gyrA 8931 p.Val544Met missense_variant 0.13
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759981 p.Ile59Phe missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 1.0
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
mmpL5 776258 c.2223C>T synonymous_variant 0.17
mmpR5 779098 p.Gly37Ser missense_variant 0.29
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 1407190 p.Thr51Ser missense_variant 0.29
atpE 1461001 c.-44G>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472944 n.1099G>T non_coding_transcript_exon_variant 0.14
rrl 1474036 n.379G>A non_coding_transcript_exon_variant 0.2
rrl 1475396 n.1739C>T non_coding_transcript_exon_variant 0.12
fabG1 1674076 p.Thr213Pro missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101974 p.Ala357Ser missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170686 c.-74G>T upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288831 p.His137Gln missense_variant 1.0
kasA 2518450 c.336C>T synonymous_variant 0.4
kasA 2518798 c.684G>T synonymous_variant 0.15
kasA 2518819 c.705C>T synonymous_variant 0.18
Rv2752c 3064695 p.Glu499Asp missense_variant 0.25
Rv2752c 3065315 p.Glu293Gln missense_variant 0.33
thyX 3067619 c.327A>C synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339248 p.Val44Ala missense_variant 0.4
Rv3083 3449694 c.1191G>T synonymous_variant 0.17
Rv3083 3449828 p.Gly442Asp missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841426 c.-6T>C upstream_gene_variant 0.11
ddn 3986983 p.Ala47Glu missense_variant 0.33
ddn 3987151 p.Lys103Ile missense_variant 0.18
clpC1 4038993 p.Phe571Tyr missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245664 p.Gly811Val missense_variant 0.29
embB 4247016 p.Ser168Leu missense_variant 0.22
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 1.0