TB-Profiler result

Run: SRR6045448
Summary

Run ID: SRR6045448

Sample name:

Date: 04-04-2023 11:59:28

Number of reads: 1857971

Percentage reads mapped: 75.93

Strain: lineage3;lineage2.2.1

Drug-resistance: Sensitive

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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 0.61
lineage2 East-Asian Beijing RD105 0.37
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.39
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.39
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
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 8405 p.His368Gln missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.97
mshA 575907 p.Ala187Val missense_variant 0.51
ccsA 620625 p.Ile245Met missense_variant 0.51
rpoB 759746 c.-61C>T upstream_gene_variant 0.68
rpoC 762434 c.-936T>G upstream_gene_variant 0.58
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775675 p.Trp936Arg missense_variant 0.46
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.23
mmpS5 778588 p.Gln106His missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305215 p.Ser762Asn missense_variant 0.66
Rv1258c 1406760 c.580_581insC frameshift_variant 0.5
embR 1416934 c.414G>A synonymous_variant 0.73
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472627 n.782G>T non_coding_transcript_exon_variant 0.15
rrl 1474134 n.477G>T non_coding_transcript_exon_variant 0.11
rrl 1474254 n.597C>A non_coding_transcript_exon_variant 0.11
rrl 1474459 n.802C>A non_coding_transcript_exon_variant 0.12
rrl 1475071 n.1414G>T non_coding_transcript_exon_variant 0.14
rrl 1475588 n.1931G>T non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.34
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 0.66
pncA 2289365 c.-125delC upstream_gene_variant 0.59
ahpC 2726105 c.-88G>A upstream_gene_variant 0.61
folC 2746268 p.Thr444Ile missense_variant 0.48
pepQ 2859624 c.795G>A synonymous_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.39
fbiB 3640671 c.-864T>C upstream_gene_variant 0.55
embC 4242075 p.Arg738Gln missense_variant 0.56
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.35
aftB 4268611 c.225delG frameshift_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.4