TB-Profiler result

Run: SRR1172744
Summary

Run ID: SRR1172744

Sample name:

Date: 03-04-2023 03:09:39

Number of reads: 1318850

Percentage reads mapped: 96.56

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.97
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.93
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.96
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 761140 p.His445Arg missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
pncA 2289038 p.Trp68Cys missense_variant 0.98 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.88 ethambutol
gid 4408095 c.107delT frameshift_variant 0.88 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
gyrB 6263 p.Asp342Tyr missense_variant 0.11
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 760581 p.Asp259Asn missense_variant 0.91
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154774 c.1338C>T synonymous_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289495 c.-254C>A upstream_gene_variant 0.1
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339553 p.Thr146Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641311 p.Asp257Asn missense_variant 0.11
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408408 c.-207delT upstream_gene_variant 0.11