TB-Profiler result

Run: SRR3105753
Summary

Run ID: SRR3105753

Sample name:

Date: 04-04-2023 05:07:43

Number of reads: 1995871

Percentage reads mapped: 99.27

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 2155142 p.Thr324Pro missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.96 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407851 c.351delG 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8948 c.1647G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490854 c.72C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620192 p.Ala101Val missense_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 767314 p.Tyr1315* stop_gained 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475332 n.1675G>T non_coding_transcript_exon_variant 0.25
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726117 c.-76T>A upstream_gene_variant 1.0
ribD 2987201 c.363C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474901 p.Ser299Arg missense_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.18
rpoA 3877963 p.Arg182Leu missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
embB 4249000 c.2487T>G synonymous_variant 1.0
aftB 4267223 c.1614C>T synonymous_variant 0.97
ubiA 4269529 p.Ala102Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0