TB-Profiler result

Run: ERR5866506
Summary

Run ID: ERR5866506

Sample name:

Date: 02-04-2023 00:43:29

Number of reads: 721960

Percentage reads mapped: 99.58

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 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
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 491213 p.Ser144Ile missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575425 c.78C>A synonymous_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576422 p.Ala359Ser missense_variant 0.14
mshA 576490 c.1143G>T synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620802 c.912C>A synonymous_variant 0.15
rpoB 759631 c.-176G>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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
mmpL5 778150 p.Gln111Lys missense_variant 0.15
mmpS5 778656 p.Ala84Pro missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302964 p.Leu12Met missense_variant 0.14
fbiC 1303028 p.Ala33Asp missense_variant 0.25
fbiC 1304856 c.1926C>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407440 c.-100C>A upstream_gene_variant 0.23
embR 1417050 p.Gly100Cys missense_variant 0.15
embR 1417058 p.Ala97Val missense_variant 0.15
embR 1417266 p.Val28Leu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472912 n.1067C>A non_coding_transcript_exon_variant 0.22
rrl 1473967 n.310G>T non_coding_transcript_exon_variant 0.17
rrl 1476507 n.2850C>A non_coding_transcript_exon_variant 0.5
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.29
rrl 1476587 n.2930C>T non_coding_transcript_exon_variant 0.25
fabG1 1673318 c.-122C>A upstream_gene_variant 0.21
fabG1 1673405 c.-35T>C upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834608 p.Arg356Leu missense_variant 0.15
rpsA 1834910 c.1373delA frameshift_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154923 p.Trp397Arg missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169626 c.987C>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518562 p.Ala150Ser missense_variant 0.17
kasA 2519067 p.Gly318Asp missense_variant 0.15
ahpC 2726358 p.Asp56Tyr missense_variant 0.17
thyX 3067916 c.30A>G synonymous_variant 0.11
thyA 3074252 p.Glu74* stop_gained 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087288 p.Gly157Cys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641571 p.Glu13* stop_gained 0.2
fbiB 3641954 c.420C>A synonymous_variant 0.2
fbiB 3642819 p.Ala429Ser missense_variant 0.2
alr 3841497 c.-77C>T upstream_gene_variant 0.18
clpC1 4038875 c.1830C>A synonymous_variant 0.67
embC 4239711 c.-152C>A upstream_gene_variant 0.14
embC 4240942 c.1080C>T synonymous_variant 0.17
embC 4241723 p.Val621Met missense_variant 0.14
embA 4242358 c.-875C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243091 p.Leu1077Ile missense_variant 0.22
embA 4243154 c.-79C>A upstream_gene_variant 0.15
embA 4243229 c.-4C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247061 p.Pro183Gln missense_variant 0.15
embB 4249497 p.Pro995Gln missense_variant 0.17
aftB 4267518 p.Thr440Lys missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267671 p.Ala389Glu missense_variant 0.15
aftB 4267889 c.948C>A synonymous_variant 0.2
aftB 4268118 p.Ala240Gly missense_variant 0.17
ethA 4326368 p.Tyr369Ser missense_variant 1.0
ethA 4327061 p.Ser138Ile missense_variant 0.14
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
pncA 2288866 c.304_375delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG conservative_inframe_deletion 1.0