TB-Profiler result

Run: ERR4831810
Summary

Run ID: ERR4831810

Sample name:

Date: 01-04-2023 21:08:11

Number of reads: 1320731

Percentage reads mapped: 90.87

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 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 0.94 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.91 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 0.93 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 7092 p.Ala618Asp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8609 c.1308G>C synonymous_variant 0.95
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 759615 c.-192A>C upstream_gene_variant 0.31
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 0.92
mmpL5 778861 c.-381G>T upstream_gene_variant 0.11
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472570 n.725G>T non_coding_transcript_exon_variant 0.17
rrs 1473222 n.1377C>A non_coding_transcript_exon_variant 0.22
rrl 1474584 n.927C>A non_coding_transcript_exon_variant 0.13
rrl 1475836 n.2179C>A non_coding_transcript_exon_variant 0.22
rrl 1476118 n.2461G>T non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.13
rrl 1476337 n.2680C>A non_coding_transcript_exon_variant 0.2
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.17
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.22
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22
rrl 1476712 n.3055C>T non_coding_transcript_exon_variant 0.14
fabG1 1673292 c.-148T>G upstream_gene_variant 0.94
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168270 c.2343G>T synonymous_variant 0.11
PPE35 2168462 c.2151C>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.31
eis 2714526 c.805_806delAC frameshift_variant 0.97
ahpC 2726341 p.Val50Gly missense_variant 0.19
Rv2752c 3065711 p.Gly161Ser missense_variant 0.87
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 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247979 p.Ile489Thr missense_variant 0.96
aftB 4266978 p.Gly620Val missense_variant 0.2
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