TB-Profiler result

Run: SRR14088389
Summary

Run ID: SRR14088389

Sample name:

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

Number of reads: 683727

Percentage reads mapped: 99.4

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 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 0.88 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrB 7175 p.Glu646* stop_gained 0.13
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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760552 p.Ser249Phe missense_variant 0.13
rpoB 761461 p.Arg552His missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763602 p.Cys78Tyr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779176 p.Ser63Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303203 c.273T>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473645 n.-12delT upstream_gene_variant 1.0
rpsA 1834803 p.Ala421Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154854 p.Met420Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726025 c.-168T>C upstream_gene_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.29
Rv2752c 3066226 c.-35G>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449122 p.Val207Met missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474874 p.Gly290Ser missense_variant 0.11
fbiB 3641654 c.120A>G synonymous_variant 0.11
embC 4240634 p.Arg258Trp missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244232 p.Ala334Thr missense_variant 0.12
embA 4244279 c.1047G>T synonymous_variant 0.14
aftB 4268838 c.-2C>G upstream_gene_variant 0.17
ubiA 4269114 p.Arg240Cys missense_variant 0.18
ubiA 4269864 c.-32delG upstream_gene_variant 0.12
ethR 4326961 c.-588G>C upstream_gene_variant 0.21
ethR 4326964 c.-585G>A upstream_gene_variant 0.21
ethR 4326970 c.-579G>T upstream_gene_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408299 c.-97A>G upstream_gene_variant 0.13