TB-Profiler result

Run: SRR6832011
Summary

Run ID: SRR6832011

Sample name:

Date: 04-04-2023 17:10:22

Number of reads: 711072

Percentage reads mapped: 99.59

Strain: lineage2.2.1

Drug-resistance: HR-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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5555 p.Gly106Ser missense_variant 0.15
gyrB 5946 p.Arg236Leu missense_variant 0.12
gyrB 6746 p.Gln503* stop_gained 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
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 576754 c.1409_1410delGC frameshift_variant 0.17
ccsA 620286 c.396G>A synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759851 c.45G>A synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766355 p.Gly996Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778776 p.Phe44Leu missense_variant 0.18
mmpR5 779183 p.Gly65Val missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800895 c.87C>A synonymous_variant 0.25
rplC 801025 p.Ala73Thr missense_variant 0.14
fbiC 1305316 p.Thr796Ala missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407274 p.Asp23Asn missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473840 n.183A>G non_coding_transcript_exon_variant 1.0
inhA 1673883 c.-319C>A upstream_gene_variant 0.2
inhA 1674930 c.729C>T synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834344 p.Asp268Gly missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918200 c.261G>A synonymous_variant 0.12
ndh 2101821 p.Lys408Glu missense_variant 0.2
ndh 2102557 c.486C>T synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155083 c.1029G>A synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986758 c.-81A>G upstream_gene_variant 0.22
Rv2752c 3065389 p.Arg268His missense_variant 0.2
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
fprA 3475189 p.Cys395Arg missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
panD 4044096 c.186C>G synonymous_variant 0.15
embC 4239737 c.-125_-124delAA upstream_gene_variant 0.14
embC 4239866 p.Ala2Ser missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244128 p.Thr299Met missense_variant 0.15
embA 4245699 p.Gly823Arg missense_variant 0.29
aftB 4267373 c.1463delT frameshift_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.89
ethA 4326657 p.Pro273Thr missense_variant 0.1
ethA 4327467 p.Glu3Lys missense_variant 0.5
ethR 4327909 p.Thr121Ser missense_variant 0.14
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
gid 4408242 c.-40T>C upstream_gene_variant 0.25