TB-Profiler result

Run: SRR1167173
Summary

Run ID: SRR1167173

Sample name:

Date: 03-04-2023 01:44:33

Number of reads: 4817610

Percentage reads mapped: 98.77

Strain: lineage4.1.1.1;lineage2.2.2

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 0.78
lineage4 Euro-American LAM;T;S;X;H None 0.21
lineage4.1 Euro-American T;X;H None 0.23
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.77
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.78
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.21
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.22
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 761110 p.Asp435Val missense_variant 0.82 rifampicin
rpoB 761139 p.His445Asp missense_variant 0.2 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.75 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.73 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.83 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.76 pyrazinamide, pyrazinamide
pncA 2288953 p.Gly97Cys missense_variant 0.24 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.54 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.51 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.73 ethionamide
gid 4407851 c.351delG frameshift_variant 0.25 streptomycin
gid 4407967 p.Leu79Ser missense_variant 0.81 streptomycin
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.76
rpoC 765150 p.Gly594Glu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.73
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2221939 p.Arg409Gln missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 0.26
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 0.81
fbiA 3641447 p.Thr302Met missense_variant 0.16
rpoA 3877553 p.Glu319Lys missense_variant 0.17
embC 4240897 c.1035C>G synonymous_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.41
embA 4243460 c.228C>T synonymous_variant 0.64
embB 4249408 c.2895G>A synonymous_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.79