TB-Profiler result

Run: ERR1577252
Summary

Run ID: ERR1577252

Sample name:

Date: 31-03-2023 14:39:51

Number of reads: 835553

Percentage reads mapped: 98.73

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
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
gyrA 9803 c.2502C>T synonymous_variant 0.25
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767076 p.Ala1236Val missense_variant 0.11
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
rplC 801279 c.471G>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.18
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.18
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.15
rrs 1472842 n.997G>A non_coding_transcript_exon_variant 0.15
rrs 1472844 n.1000delG non_coding_transcript_exon_variant 0.15
rrs 1472847 n.1002G>T non_coding_transcript_exon_variant 0.15
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.15
rrs 1472856 n.1012_1013insCGA non_coding_transcript_exon_variant 0.15
rrs 1472860 n.1016G>C non_coding_transcript_exon_variant 0.18
rrs 1472863 n.1018T>G non_coding_transcript_exon_variant 0.15
rrs 1472866 n.1021C>T non_coding_transcript_exon_variant 0.15
rrs 1472868 n.1023T>C non_coding_transcript_exon_variant 0.15
rrs 1472870 n.1025T>G non_coding_transcript_exon_variant 0.14
rrs 1472872 n.1027G>A non_coding_transcript_exon_variant 0.14
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.14
rrs 1472879 n.1034T>A non_coding_transcript_exon_variant 0.14
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.14
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.14
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.15
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.15
rrl 1474344 n.687G>A non_coding_transcript_exon_variant 0.14
rrl 1474828 n.1171G>A non_coding_transcript_exon_variant 0.17
rrl 1476467 n.2810A>G non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917875 c.-65T>C upstream_gene_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155735 p.Met126Lys missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169291 p.Val441Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519234 p.Glu374Lys missense_variant 0.11
Rv2752c 3067060 c.-869C>G upstream_gene_variant 0.12
thyX 3067194 c.752G>T stop_lost&splice_region_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339246 c.129C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475298 p.Arg431Pro missense_variant 0.29
Rv3236c 3612199 c.918G>T synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641428 p.Ala296Thr missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.13
rpoA 3878569 c.-63_-62insG upstream_gene_variant 0.14
rpoA 3878580 c.-74_-73insCAACCCA upstream_gene_variant 0.14
embC 4242576 p.Gln905Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247601 p.Leu363Pro missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268282 c.555G>A synonymous_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