TB-Profiler result

Run: SRR2100848
Summary

Run ID: SRR2100848

Sample name:

Date: 03-04-2023 23:19:40

Number of reads: 2061083

Percentage reads mapped: 99.2

Strain: lineage3.1

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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi 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
katG 2155258 p.Gly285Asp missense_variant 0.14 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4408100 c.102dupG frameshift_variant 0.97 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 8486 c.1185T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575431 c.84C>T synonymous_variant 0.13
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 1.0
rpoC 764666 p.Gly433Ser 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.26
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 2169317 c.1296C>T synonymous_variant 0.26
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
pncA 2289047 c.195C>T synonymous_variant 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339737 p.Thr207Ile missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.1
clpC1 4038857 c.1848C>A synonymous_variant 0.35
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242555 p.Leu898Ser missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243378 p.Ser49Thr missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0