TB-Profiler result

Run: SRR14088379
Summary

Run ID: SRR14088379

Sample name:

Date: 03-04-2023 09:46:20

Number of reads: 2145135

Percentage reads mapped: 99.72

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288868 p.Val125Gly missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 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 1.0
gyrA 7581 p.Asp94Cys missense_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.26
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759988 p.Ser61* stop_gained 0.25
rpoB 759991 p.Pro62Gln missense_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763381 c.12C>A synonymous_variant 0.13
rpoC 763397 p.Leu10Phe missense_variant 0.13
rpoC 764817 p.Val483Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461187 p.Arg48Leu missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471889 n.44G>T non_coding_transcript_exon_variant 0.25
rrs 1472782 n.937G>T non_coding_transcript_exon_variant 1.0
rrl 1474311 n.654G>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168442 p.Trp724Leu missense_variant 0.25
Rv1979c 2222156 p.Pro337Thr missense_variant 0.13
Rv1979c 2222535 c.630C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223303 c.-139G>T upstream_gene_variant 0.12
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086703 c.-117T>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0
rpoA 3878646 c.-139G>T upstream_gene_variant 0.17
clpC1 4039473 p.Arg411Leu missense_variant 0.19
panD 4044023 c.259C>T synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326341 p.Pro378His missense_variant 0.19
ethA 4326389 p.Asp362Val missense_variant 0.15
ethA 4326967 p.Glu169Asp missense_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0
whiB6 4337780 c.-383_*390del transcript_ablation 1.0