TB-Profiler result

Run: SRR7517756
Summary

Run ID: SRR7517756

Sample name:

Date: 04-04-2023 19:36:16

Number of reads: 1963824

Percentage reads mapped: 97.41

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 0.99
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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
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
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
ccsA 620778 c.888T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763073 p.Asp1089Glu missense_variant 0.14
rpoB 763147 p.Ser1114* stop_gained 0.31
rpoC 763478 p.Arg37Ser missense_variant 0.17
rpoC 765140 p.Glu591Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.96
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776142 p.Gly780Val missense_variant 0.17
mmpL5 776459 c.2022G>T synonymous_variant 0.2
mmpL5 776911 p.Glu524* stop_gained 0.29
mmpL5 776951 c.1530G>T synonymous_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471795 n.-51C>A upstream_gene_variant 0.5
rrs 1471902 n.57C>T non_coding_transcript_exon_variant 0.29
rrs 1471975 n.130G>A non_coding_transcript_exon_variant 0.29
rrs 1472849 n.1004C>A non_coding_transcript_exon_variant 0.33
rrs 1472902 n.1057C>A non_coding_transcript_exon_variant 0.33
rrs 1472907 n.1062C>A non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.67
rrl 1474604 n.947G>T non_coding_transcript_exon_variant 0.4
rrl 1474619 n.962G>A non_coding_transcript_exon_variant 0.4
rrl 1474895 n.1238C>A non_coding_transcript_exon_variant 0.29
rrl 1474956 n.1299C>A non_coding_transcript_exon_variant 0.22
rrl 1475514 n.1857G>T non_coding_transcript_exon_variant 0.5
inhA 1673493 c.-709C>A upstream_gene_variant 0.36
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102727 p.His106Asn missense_variant 0.19
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168838 p.Pro592Gln missense_variant 0.2
PPE35 2168927 c.1686G>T synonymous_variant 0.2
PPE35 2169796 p.Gly273Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289887 c.-649_-647delCCG 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
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
fbiB 3640581 c.-954C>A upstream_gene_variant 1.0
alr 3841588 c.-168C>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249739 p.Ala1076Thr missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268614 p.Gly75Trp missense_variant 0.2
ethA 4326403 p.Asp357Glu missense_variant 0.14
ethA 4327265 p.Thr70Ile missense_variant 0.15
whiB6 4338501 c.21A>G synonymous_variant 0.1
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