TB-Profiler result

Run: SRR12708376
Summary

Run ID: SRR12708376

Sample name:

Date: 02-08-2023 14:42:07

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.4.1.1;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 0.29
lineage4 Euro-American LAM;T;S;X;H None 0.76
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage4.4 Euro-American S;T None 0.69
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
lineage4.4.1.1 Euro-American S;Orphans None 0.7
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 0.26 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.32 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.21 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.52 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.34 isoniazid, ethionamide
pncA 2289253 c.-12T>C upstream_gene_variant 0.23 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.24 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 0.32 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
gyrB 5462 p.Val75Leu missense_variant 0.81
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.34
mshA 575907 p.Ala187Val missense_variant 0.35
ccsA 620625 p.Ile245Met missense_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpL5 777416 c.1065G>T synonymous_variant 0.65
mmpS5 778979 c.-74G>T upstream_gene_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.65
katG 2154724 p.Arg463Leu missense_variant 0.32
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2168479 p.Thr712Pro missense_variant 0.69
PPE35 2169840 p.Gly258Asp missense_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065023 p.Pro390Leu missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 0.75
Rv3083 3448608 c.105G>A synonymous_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.48
Rv3236c 3612665 p.Val151Ala missense_variant 0.7
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19
rpoA 3877949 p.Thr187Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.41
aftB 4267647 p.Asp397Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.21
gid 4407927 p.Glu92Asp missense_variant 0.23