TB-Profiler result

Run: SRR6855878

Summary

Run ID: SRR6855878

Sample name:

Date: 04-04-2023 17:48:48

Number of reads: 344754

Percentage reads mapped: 99.69

Strain: lineage2.2.1

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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
tlyA 1918499 c.564delG frameshift_variant 0.14 capreomycin
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 6534 p.Ala432Asp missense_variant 0.11
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 491735 p.Arg318His missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576113 p.Arg256Trp missense_variant 0.17
mshA 576365 p.Phe340Ile missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762432 p.Gly876Arg missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775869 p.Ile871Thr missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777157 p.Arg442Trp missense_variant 0.29
mmpS5 778797 p.Ile37Leu missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800678 c.-131C>T upstream_gene_variant 0.13
fbiC 1302940 p.Pro4Ser missense_variant 0.14
fbiC 1304128 p.Gln400Glu missense_variant 0.11
Rv1258c 1406253 p.Gly363Val missense_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473460 n.-198G>T upstream_gene_variant 0.12
rrl 1474026 n.369C>A non_coding_transcript_exon_variant 0.5
rrl 1474641 n.984G>T non_coding_transcript_exon_variant 0.13
rrl 1475648 n.1991A>G non_coding_transcript_exon_variant 0.11
rrl 1475954 n.2297A>G non_coding_transcript_exon_variant 0.15
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.22
fabG1 1673826 c.389delA frameshift_variant 0.2
inhA 1674210 c.9A>C synonymous_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834403 c.865delC frameshift_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101901 p.Lys381Arg missense_variant 0.1
ndh 2102012 p.Ala344Val missense_variant 0.12
katG 2153911 p.Leu734His missense_variant 0.14
katG 2154302 c.1810T>C synonymous_variant 0.12
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
kasA 2518024 c.-91C>A upstream_gene_variant 0.12
eis 2715544 c.-213delC upstream_gene_variant 0.11
folC 2747229 p.Tyr124His missense_variant 0.14
pepQ 2860216 p.Ala68Val missense_variant 0.15
Rv2752c 3065416 p.Val259Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087752 c.933C>T synonymous_variant 0.12
Rv3083 3449471 p.Thr323Ile missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474717 p.Asp237Glu missense_variant 0.13
whiB7 3568467 p.Phe71Leu missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640391 c.-152C>A upstream_gene_variant 0.12
clpC1 4038253 p.Phe818Leu missense_variant 0.14
clpC1 4038342 p.Lys788Arg missense_variant 0.17
clpC1 4039260 p.Glu482Gly missense_variant 0.1
panD 4043978 c.300_303delATAC frameshift_variant 0.14
embC 4241860 c.1998C>G synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243587 p.Arg119Ser missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268348 c.489G>T synonymous_variant 0.12
ubiA 4269793 p.Val14Ala missense_variant 0.13
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
gid 4408229 c.-27A>G upstream_gene_variant 0.2
gid 4408440 c.-238C>A upstream_gene_variant 0.15