TB-Profiler result

Run: SRR7657748
Summary

Run ID: SRR7657748

Sample name:

Date: 04-04-2023 20:11:26

Number of reads: 6114110

Percentage reads mapped: 99.65

Strain: lineage4.2.1;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 0.82
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.2 Euro-American H;T;LAM None 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage4.2.1 Euro-American (TUR) H3;H4 None 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 760663 p.Ala286Val missense_variant 0.19 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.19 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.16 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288806 p.Ala146Thr missense_variant 0.13 pyrazinamide
pncA 2288820 p.Gln141Pro missense_variant 0.84 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.81 ethambutol
embB 4247729 p.Gly406Cys missense_variant 0.24 ethambutol
ethA 4326463 c.1010delT frameshift_variant 0.83 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.83
mshA 575907 p.Ala187Val missense_variant 0.8
ccsA 619969 p.Val27Ile missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.86
rpoB 759940 p.Pro45Leu missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
mmpL5 776182 p.Asp767Asn missense_variant 0.82
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.83
PPE35 2167926 p.Leu896Ser missense_variant 0.86
PPE35 2169879 p.Phe245Cys missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715340 c.-8C>T upstream_gene_variant 0.19
ribD 2986827 c.-12G>A upstream_gene_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 0.85
ald 3086742 c.-78A>C upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243346 c.114A>G synonymous_variant 0.79
embA 4243460 c.228C>T synonymous_variant 0.8
embB 4249594 c.3081G>A synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.85
ethA 4328376 c.-903G>C upstream_gene_variant 0.16
whiB6 4338371 p.Thr51Pro missense_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 0.84