TB-Profiler result

Run: SRR6339664
Summary

Run ID: SRR6339664

Sample name:

Date: 04-04-2023 13:29:51

Number of reads: 1263407

Percentage reads mapped: 99.28

Strain: lineage2.1

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
lineage2 East-Asian Beijing RD105 0.96
lineage2.1 East-Asian (non-Beijing) None None 0.98
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 0.88 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288819 c.422delA frameshift_variant 0.96 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.95 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 6112 p.Met291Ile missense_variant 0.27
gyrB 6227 p.Lys330* stop_gained 0.17
gyrB 7109 p.Thr624Pro missense_variant 0.2
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 490946 p.Leu55Pro missense_variant 0.12
fgd1 491315 p.Gly178Ala missense_variant 0.25
fgd1 491404 p.Met208Leu missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoB 761253 p.Pro483Ser missense_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765121 c.1752G>A synonymous_variant 0.96
rpoC 766922 p.Glu1185Lys missense_variant 0.48
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778706 p.Val67Gly missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781633 p.Lys25Arg missense_variant 0.11
fbiC 1302789 c.-142C>T upstream_gene_variant 0.98
fbiC 1304443 p.Ala505Thr missense_variant 1.0
embR 1417200 p.Val50Leu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472746 n.901A>T non_coding_transcript_exon_variant 0.17
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.33
rrl 1475482 n.1825A>G non_coding_transcript_exon_variant 0.33
rrl 1475909 n.2252A>T non_coding_transcript_exon_variant 0.3
fabG1 1673560 p.Lys41Gln missense_variant 0.11
fabG1 1674101 p.Val221Gly missense_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834501 c.960G>A synonymous_variant 0.92
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103064 c.-22A>G upstream_gene_variant 0.12
katG 2154362 p.Phe584Val missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155891 p.Asp74Ala missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169063 p.Met517Lys missense_variant 0.14
PPE35 2169144 p.Val490Glu missense_variant 0.39
Rv1979c 2223293 c.-129A>G 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
fbiA 3641272 p.Ser244Thr missense_variant 0.17
clpC1 4038883 p.Gly608Ser missense_variant 0.23
clpC1 4040841 c.-138delG upstream_gene_variant 0.87
embC 4240418 p.Gly186Cys missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4245457 p.Glu742Ala missense_variant 0.33
embB 4246088 c.-426A>G upstream_gene_variant 0.91
embB 4247039 p.Phe176Val missense_variant 0.33
embB 4249781 p.Ser1090Ala missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.82
ubiA 4269387 p.Glu149Asp missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ethA 4326450 p.Thr342Ser missense_variant 0.11
ethA 4327106 p.His123Pro missense_variant 0.13
ethA 4328025 c.-552T>G upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.11