TB-Profiler result

Run: ERR4799902
Summary

Run ID: ERR4799902

Sample name:

Date: 01-04-2023 09:27:21

Number of reads: 2884380

Percentage reads mapped: 99.49

Strain: lineage2.2.1;lineage1.2.2.2

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 0.76
lineage1 Indo-Oceanic EAI RD239 0.22
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.73
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.23
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.69
lineage1.2.2.2 Indo-Oceanic NA RD239 0.21
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673424 c.-16A>G upstream_gene_variant 0.16 isoniazid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.16 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 0.27 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.22 pyrazinamide, pyrazinamide
pncA 2289228 p.Ile5Ser missense_variant 0.78 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.76 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.81 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.65 ethambutol
embB 4247495 p.Asp328Tyr missense_variant 0.42 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 5075 c.-165C>T upstream_gene_variant 0.3
gyrB 6112 p.Met291Ile missense_variant 0.24
gyrA 7268 c.-34C>T upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7401 p.Ser34Arg missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.23
gyrA 9143 c.1842T>C synonymous_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.84
fgd1 491742 c.960T>C synonymous_variant 0.96
mshA 575907 p.Ala187Val missense_variant 0.72
ccsA 620625 p.Ile245Met missense_variant 0.69
rpoB 760215 p.Asn137Asp missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.19
rpoC 763886 c.517C>A synonymous_variant 0.22
rpoC 764651 p.Ser428Ala missense_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.74
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78
embR 1417019 p.Cys110Tyr missense_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474036 n.379G>T non_coding_transcript_exon_variant 0.17
rrl 1475316 n.1659G>T non_coding_transcript_exon_variant 0.13
rrl 1475619 n.1962C>A non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.37
Rv1979c 2222308 p.Asp286Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21
ahpC 2726418 p.Glu76Lys missense_variant 0.21
thyX 3067949 c.-4C>T upstream_gene_variant 0.79
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.16
fprA 3475159 p.Asn385Asp missense_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81
clpC1 4040517 p.Val63Ala missense_variant 0.28
clpC1 4040719 c.-15A>G upstream_gene_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.24
embC 4241022 p.Ala387Val missense_variant 0.79
embC 4241042 p.Asn394Asp missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.72
embA 4245969 p.Pro913Ser missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 0.17
embB 4247847 p.Gln445Arg missense_variant 0.74
aftB 4267647 p.Asp397Gly missense_variant 0.73
aftB 4267960 p.Val293Met missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 0.24
ethA 4326148 c.1326G>T synonymous_variant 0.12
ethA 4326439 p.Asn345Lys missense_variant 0.18
ethA 4327126 p.Trp116Cys missense_variant 0.29
whiB6 4338203 p.Arg107Cys missense_variant 0.19
whiB6 4338292 p.Ala77Val missense_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407620 p.Tyr195His missense_variant 0.71
gid 4407848 p.Ala119Thr missense_variant 0.29
gid 4407873 c.330G>T synonymous_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 0.75