TB-Profiler result

Run: ERR4831889
Summary

Run ID: ERR4831889

Sample name:

Date: 01-04-2023 21:11:26

Number of reads: 823399

Percentage reads mapped: 99.4

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 781822 p.Lys88Arg 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 6828 p.Met530Thr missense_variant 0.22
gyrB 6927 p.Leu563Trp missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8578 p.Asp426Ala missense_variant 0.13
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 759794 c.-13G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763930 p.Glu187Asp missense_variant 0.12
rpoC 765651 p.Gln761Arg missense_variant 0.1
rpoC 766948 c.3579G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775966 p.Ala839Ser missense_variant 0.14
mmpL5 775970 c.2511G>C synonymous_variant 0.14
mmpL5 775975 c.2506T>C synonymous_variant 0.14
mmpL5 775981 p.Leu834Met missense_variant 0.13
mmpL5 775994 p.Ile829Leu missense_variant 0.14
mmpL5 775997 c.2484T>G synonymous_variant 0.14
mmpL5 776000 p.Leu827Ile missense_variant 0.15
mmpL5 776005 p.Ile826Leu missense_variant 0.15
mmpL5 776009 c.2472A>G synonymous_variant 0.15
mmpL5 776030 c.2451G>C synonymous_variant 0.11
mmpL5 776045 c.2436G>C synonymous_variant 0.12
mmpL5 776053 c.2428T>C synonymous_variant 0.12
mmpL5 776075 c.2406C>G synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776271 p.Lys737Met missense_variant 0.29
mmpS5 778761 p.Glu49* stop_gained 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302882 c.-49C>A upstream_gene_variant 0.11
fbiC 1303913 p.Gly328Val missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417353 c.-6C>T upstream_gene_variant 0.1
embR 1417393 c.-46G>A upstream_gene_variant 0.12
embR 1417478 c.-131C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471748 n.-98C>T upstream_gene_variant 0.14
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.12
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.18
rrs 1473186 n.1341A>G non_coding_transcript_exon_variant 0.22
rrl 1474482 n.825G>T non_coding_transcript_exon_variant 0.22
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.18
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.17
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.12
rrl 1474999 n.1342C>A non_coding_transcript_exon_variant 0.25
rrl 1476409 n.2752T>C non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.15
fabG1 1674059 p.Pro207Gln missense_variant 0.11
inhA 1674210 c.9A>C synonymous_variant 1.0
rpsA 1833473 c.-69C>A upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102965 c.78G>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154904 p.Glu403Gly missense_variant 0.12
katG 2155608 c.504C>T synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168885 c.1728A>T synonymous_variant 0.25
PPE35 2168933 p.Ile560Met missense_variant 0.12
PPE35 2169496 p.Asp373Asn missense_variant 0.11
PPE35 2169622 p.Phe331Leu missense_variant 0.18
PPE35 2170589 c.24G>T synonymous_variant 0.14
Rv1979c 2222992 p.Ala58Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.25
folC 2747066 p.Gly178Asp missense_variant 0.11
pepQ 2859570 c.849C>T synonymous_variant 0.12
Rv2752c 3064556 p.Arg546Cys missense_variant 0.12
thyA 3073718 p.Asp252Tyr missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612092 p.Gly342Val missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641625 p.Ala31Thr missense_variant 1.0
alr 3841494 c.-74G>T upstream_gene_variant 0.12
rpoA 3878331 c.177A>G synonymous_variant 0.1
ddn 3987026 c.183C>A synonymous_variant 0.14
panD 4044155 p.Gln43Lys missense_variant 0.12
embC 4241561 p.Arg567Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244976 p.Gly582Arg missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327639 p.Ala31Ser missense_variant 0.12
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