TB-Profiler result

Run: ERR5863845

Summary

Run ID: ERR5863845

Sample name:

Date: 01-04-2023 22:56:45

Number of reads: 733467

Percentage reads mapped: 99.47

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 761078 p.Phe424Leu missense_variant 0.14 rifampicin
rpoB 761155 p.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T 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
gyrB 6242 p.Arg335Ser missense_variant 0.18
gyrB 6447 p.Ala403Glu missense_variant 0.22
gyrB 6829 p.Met530Ile missense_variant 0.18
gyrB 6959 p.Gln574* stop_gained 0.15
gyrB 7082 p.Glu615* stop_gained 0.15
gyrA 7216 c.-86G>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7731 p.Glu144* stop_gained 0.4
gyrA 7745 p.Glu148Asp missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9394 p.Ser698* stop_gained 0.2
gyrA 9508 p.Ala736Glu missense_variant 0.2
fgd1 491092 p.Gly104Cys missense_variant 0.18
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 762923 c.-447C>A upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767015 p.Ala1216Thr missense_variant 0.14
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
fbiC 1304635 p.Gln569* stop_gained 0.19
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471704 n.-142C>A upstream_gene_variant 0.17
rrs 1472800 n.955C>A non_coding_transcript_exon_variant 0.22
rrl 1474522 n.865C>T non_coding_transcript_exon_variant 0.2
rrl 1475625 n.1969delT non_coding_transcript_exon_variant 0.67
inhA 1674072 c.-130C>A upstream_gene_variant 0.17
rpsA 1834001 p.Glu154* stop_gained 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834191 p.Ser217Tyr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102123 p.Pro307His missense_variant 0.12
katG 2154536 p.Glu526* stop_gained 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154891 c.1221G>A synonymous_variant 0.22
katG 2155825 p.Gly96Val missense_variant 0.15
PPE35 2167813 p.Gln934Lys missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168921 c.1692G>A synonymous_variant 0.2
Rv1979c 2222280 c.885C>A synonymous_variant 0.17
Rv1979c 2222641 p.Ser175* stop_gained 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223299 c.-135G>T upstream_gene_variant 0.17
pncA 2289960 c.-719C>G upstream_gene_variant 0.15
kasA 2518240 c.126C>A synonymous_variant 0.2
ahpC 2726716 p.Ala175Glu missense_variant 0.13
ribD 2986777 c.-62C>A upstream_gene_variant 0.2
Rv2752c 3065150 c.1041_1042insA frameshift_variant 1.0
Rv2752c 3067187 c.-997_-996insG upstream_gene_variant 1.0
thyA 3073815 c.657G>A synonymous_variant 0.13
thyA 3073855 p.Cys206Phe missense_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448342 c.-162A>G upstream_gene_variant 0.12
Rv3083 3449116 p.Ala205Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568757 c.-78A>T upstream_gene_variant 0.13
Rv3236c 3612289 c.828G>T synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641130 c.-405A>G upstream_gene_variant 0.11
alr 3841453 c.-33G>T upstream_gene_variant 0.17
rpoA 3877867 p.Thr214Met missense_variant 0.14
clpC1 4039864 p.Asp281Tyr missense_variant 0.18
clpC1 4039915 p.Asp264Tyr missense_variant 0.18
embC 4239665 c.-198G>A upstream_gene_variant 0.13
embC 4240160 p.Thr100Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246207 p.Pro992Gln missense_variant 0.17
aftB 4267320 p.Asp506Gly missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267915 p.Pro308Thr missense_variant 0.15
ethA 4326669 p.Gln269Lys missense_variant 0.14
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407537 c.666G>T synonymous_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0