TB-Profiler result

Run: SRR3743376
Summary

Run ID: SRR3743376

Sample name:

Date: 04-04-2023 05:41:20

Number of reads: 2245544

Percentage reads mapped: 99.47

Strain: lineage4.2.1;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 0.79
lineage4 Euro-American LAM;T;S;X;H None 0.19
lineage4.2 Euro-American H;T;LAM None 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.2
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 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.7 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.3 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.2 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.8 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289201 p.Cys14Tyr missense_variant 0.15 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.2 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.76 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.88 para-aminosalicylic_acid
embB 4247402 p.Ser297Ala missense_variant 0.17 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
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 0.3
fgd1 491742 c.960T>C synonymous_variant 0.85
mshA 575907 p.Ala187Val missense_variant 0.8
ccsA 619969 p.Val27Ile missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.79
rpoC 763031 c.-339T>C upstream_gene_variant 0.83
rpoC 764817 p.Val483Gly missense_variant 0.17
rpoC 766645 p.Glu1092Asp missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.78
mmpL5 776182 p.Asp767Asn missense_variant 0.73
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 0.7
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.7
PPE35 2169835 p.Gly260* stop_gained 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81
fbiA 3640675 p.Val45Ile missense_variant 0.24
fbiB 3641810 c.276G>C synonymous_variant 0.79
alr 3840391 p.Asp344Asn missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.9
embB 4249594 c.3081G>A synonymous_variant 0.23
aftB 4267647 p.Asp397Gly missense_variant 0.85
ethA 4326339 p.Asn379Asp missense_variant 0.62
ethA 4326632 p.His281Pro missense_variant 0.17
ethA 4328376 c.-903G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.72
gid 4407927 p.Glu92Asp missense_variant 0.76