TB-Profiler result

Run: SRR413216
Summary

Run ID: SRR413216

Sample name:

Date: 04-04-2023 07:50:01

Number of reads: 3134182

Percentage reads mapped: 99.19

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 761140 p.His445Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.1 isoniazid, ethionamide
katG 2155169 p.Ser315Arg missense_variant 0.23 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
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 759831 p.Thr9Pro missense_variant 0.29
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765088 c.1719G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775727 c.2752_2753delAC frameshift_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155140 c.972C>T synonymous_variant 1.0
katG 2155832 p.Asp94Asn missense_variant 0.47
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.16
PPE35 2169379 p.Phe412Val missense_variant 0.23
PPE35 2169866 c.747G>C synonymous_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.19
ribD 2987307 p.Ala157Pro missense_variant 0.13
Rv2752c 3064552 p.Arg547Pro missense_variant 0.24
thyX 3067995 c.-50A>C upstream_gene_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.16
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4039363 p.Ala448Pro missense_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.39
embC 4239842 c.-21C>A upstream_gene_variant 0.11
embC 4242476 p.Pro872Ala missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.4
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.23
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