TB-Profiler result

Run: ERR4830534
Summary

Run ID: ERR4830534

Sample name:

Date: 01-04-2023 20:16:39

Number of reads: 324665

Percentage reads mapped: 99.52

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.27 isoniazid, ethionamide
katG 2155732 p.Gln127Pro missense_variant 0.36 isoniazid
ethA 4326830 c.643delC frameshift_variant 0.12 ethionamide
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 7661 c.362delA frameshift_variant 0.18
gyrA 7678 p.Ala126Val missense_variant 0.18
gyrA 8295 c.996_997delCA frameshift_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490686 c.-97G>T upstream_gene_variant 0.25
fgd1 490747 c.-36C>A upstream_gene_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576488 p.Val381His missense_variant 0.29
ccsA 619713 c.-178C>T upstream_gene_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763398 p.Leu10Pro missense_variant 0.12
rpoC 764422 c.1053C>T synonymous_variant 0.29
rpoC 766707 p.Glu1113Gly missense_variant 0.13
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 777736 p.Phe249Leu missense_variant 0.13
mmpL5 778019 c.461delC frameshift_variant 0.13
mmpL5 778101 p.Gln127Arg missense_variant 0.12
mmpL5 778837 c.-357C>T upstream_gene_variant 0.17
mmpS5 778961 c.-56C>T upstream_gene_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781685 c.126G>A synonymous_variant 0.11
fbiC 1302982 p.Pro18Ser missense_variant 0.13
fbiC 1303561 p.Met211Val missense_variant 0.18
fbiC 1303877 p.Ala316Val missense_variant 0.14
fbiC 1305099 c.2169T>A synonymous_variant 0.17
fbiC 1305106 c.2176C>T synonymous_variant 0.2
fbiC 1305248 p.Ala773Val missense_variant 0.15
Rv1258c 1406439 p.Ala301Val missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461123 p.Gly27Arg missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472097 n.252T>C non_coding_transcript_exon_variant 0.11
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.1
rrl 1473753 n.96A>G non_coding_transcript_exon_variant 0.15
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.11
rpsA 1833512 c.-30A>G upstream_gene_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101806 p.Thr413Ser missense_variant 0.14
ndh 2101913 p.Ser377Leu missense_variant 0.11
ndh 2102175 p.Ala290Ser missense_variant 0.22
ndh 2102685 p.Gly120Ser missense_variant 1.0
ndh 2102686 c.357G>A synonymous_variant 0.2
ndh 2103031 p.Gln4His missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168291 p.Leu774Phe missense_variant 0.11
PPE35 2170780 c.-168G>T upstream_gene_variant 0.16
Rv1979c 2222297 p.Lys290* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288768 c.474C>T synonymous_variant 0.12
kasA 2518678 c.567_568insACCGCCGCAGAC conservative_inframe_insertion 0.25
kasA 2518683 p.Ala190Gly missense_variant 0.25
kasA 2518692 p.Ala193Gly missense_variant 0.25
eis 2714707 p.Gly209Ala missense_variant 0.12
pepQ 2860263 c.156C>G synonymous_variant 0.15
Rv2752c 3065487 c.705T>C synonymous_variant 0.14
thyA 3073703 p.Ile257Phe missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448624 p.Leu41Met missense_variant 0.14
fprA 3473831 c.-176G>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642338 c.804C>T synonymous_variant 0.2
rpoA 3877696 p.Thr271Ile missense_variant 0.11
clpC1 4038495 p.Arg737Gln missense_variant 0.13
panD 4044166 p.Leu39Pro missense_variant 0.14
panD 4044402 c.-121T>C upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245145 p.Gln638Leu missense_variant 0.12
embA 4245930 p.Gly900Ser missense_variant 0.22
embB 4246538 p.Lys9* stop_gained 0.14
embB 4247851 c.1338C>A synonymous_variant 0.15
embB 4249393 p.Trp960Cys missense_variant 0.13
embB 4249479 p.Ala989Gly missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327515 c.-42A>C upstream_gene_variant 0.29
ethA 4327944 c.-471G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0