TB-Profiler result

Run: SRR6831909
Summary

Run ID: SRR6831909

Sample name:

Date: 04-04-2023 17:06:41

Number of reads: 666393

Percentage reads mapped: 99.54

Strain: lineage2.2

Drug-resistance: Other

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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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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
rpsL 781687 p.Lys43Arg missense_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 7773 p.Gly158Ser missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490682 c.-101C>T upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576091 c.744C>A synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764664 p.Val432Ala missense_variant 0.17
rpoC 765035 p.Arg556Ser missense_variant 0.11
rpoC 765846 p.Asn826Ile missense_variant 0.25
rpoC 766637 p.Lys1090* stop_gained 0.17
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781487 c.-73C>G upstream_gene_variant 0.22
rplC 800759 c.-50C>T upstream_gene_variant 0.15
fbiC 1302811 c.-120G>A upstream_gene_variant 0.13
fbiC 1303493 p.Leu188Ser missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472033 n.188A>T non_coding_transcript_exon_variant 0.2
rrl 1473739 n.82G>A non_coding_transcript_exon_variant 0.13
rrl 1474309 n.652G>T non_coding_transcript_exon_variant 0.2
rrl 1474935 n.1278A>G non_coding_transcript_exon_variant 0.15
rrl 1474948 n.1291C>T non_coding_transcript_exon_variant 0.17
inhA 1674244 p.Ile15Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102995 c.48A>T synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154775 p.Ser446Thr missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725945 c.-248G>A upstream_gene_variant 0.22
pepQ 2859410 p.Arg337Cys missense_variant 0.18
pepQ 2859423 c.996C>T synonymous_variant 0.17
Rv2752c 3065439 c.753C>T synonymous_variant 0.2
thyA 3073805 p.Glu223Lys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087689 c.870G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613315 c.-199T>C upstream_gene_variant 0.22
rpoA 3877590 c.918G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245196 p.Ile655Thr missense_variant 0.5
embA 4245264 p.Asp678Tyr missense_variant 0.17
embB 4247407 c.894G>A synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268906 c.-70C>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0