TB-Profiler result

Run: SRR6484856
Summary

Run ID: SRR6484856

Sample name:

Date: 04-04-2023 14:49:21

Number of reads: 1521200

Percentage reads mapped: 99.62

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.Asp435Val missense_variant 0.95 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 0.92 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 5752 c.513G>A synonymous_variant 0.11
gyrB 5931 p.Lys231Arg missense_variant 0.11
gyrB 6681 p.Leu481Pro missense_variant 0.14
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 491082 c.300T>C synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576480 p.Pro378His missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.14
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 776182 p.Asp767Asn missense_variant 1.0
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
atpE 1461075 p.Ile11Phe missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472447 n.602C>A non_coding_transcript_exon_variant 0.17
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15
rrs 1472589 n.744A>G non_coding_transcript_exon_variant 0.11
rrs 1473258 n.1413T>C non_coding_transcript_exon_variant 0.12
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.12
rrl 1474628 n.971C>T non_coding_transcript_exon_variant 0.17
rrl 1475653 n.1996A>G non_coding_transcript_exon_variant 0.13
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168017 p.Ile866Val missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170065 p.Ala183Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475174 p.Lys390Glu missense_variant 0.11
whiB7 3568635 c.45G>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.93
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249321 c.2808A>G synonymous_variant 0.12
embB 4249336 c.2823C>G synonymous_variant 0.14
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
gid 4408355 c.-153A>C upstream_gene_variant 0.22