TB-Profiler result

Run: SRR5535694

Summary

Run ID: SRR5535694

Sample name:

Date: 04-04-2023 10:38:14

Number of reads: 1537249

Percentage reads mapped: 98.9

Strain: lineage2.2.1

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 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5791 p.Glu184Asp missense_variant 0.11
gyrB 6060 p.Ser274Ile missense_variant 0.25
gyrB 6429 p.Glu397Gly missense_variant 0.2
gyrA 7301 c.-1G>A upstream_gene_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
gyrA 9770 c.2469C>A synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575782 c.435G>T synonymous_variant 0.18
ccsA 619735 c.-156G>T upstream_gene_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761848 p.Cys681Tyr missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765763 c.2394G>T synonymous_variant 0.18
rpoC 766370 p.Gln1001* stop_gained 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800651 c.-158G>A upstream_gene_variant 0.13
rplC 801360 p.Lys184Asn missense_variant 0.17
fbiC 1304759 p.Pro610Gln missense_variant 0.14
fbiC 1304789 p.Ala620Asp missense_variant 0.12
Rv1258c 1406405 c.936G>T synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417103 p.Leu82Arg missense_variant 0.18
atpE 1461260 c.216G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472924 n.1079G>T non_coding_transcript_exon_variant 0.5
rrs 1473354 n.1509G>T non_coding_transcript_exon_variant 0.17
rrl 1475369 n.1712G>A non_coding_transcript_exon_variant 0.4
rrl 1475728 n.2071C>T non_coding_transcript_exon_variant 0.33
inhA 1674967 p.Asp256Asn missense_variant 0.33
rpsA 1834003 p.Glu154Asp missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 0.92
rpsA 1834668 p.Ala376Glu missense_variant 0.15
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918080 c.141C>A synonymous_variant 0.22
tlyA 1918454 p.Ser172Leu missense_variant 0.17
ndh 2102378 p.Pro222Gln missense_variant 0.13
ndh 2102702 p.Ser114Ile missense_variant 0.15
ndh 2102723 p.Thr107Asn missense_variant 0.2
ndh 2102744 p.Val100Gly missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155436 p.Gly226Trp missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169023 c.1590G>A synonymous_variant 1.0
PPE35 2169552 p.Pro354His missense_variant 0.12
PPE35 2170457 c.156G>T synonymous_variant 0.18
Rv1979c 2222696 p.Arg157Trp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519128 c.1014G>C synonymous_variant 0.12
kasA 2519131 c.1017G>C synonymous_variant 0.12
eis 2714605 p.Ala243Val missense_variant 0.29
eis 2714871 c.462G>T synonymous_variant 0.2
eis 2715228 c.105C>A synonymous_variant 0.11
eis 2715466 c.-134C>T upstream_gene_variant 0.14
ahpC 2726055 c.-138G>T upstream_gene_variant 0.14
Rv2752c 3065768 p.Glu142Lys missense_variant 0.29
thyX 3068012 c.-67G>T upstream_gene_variant 0.13
thyA 3073707 c.765G>T synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087404 c.585G>A synonymous_variant 0.13
ald 3087777 p.Tyr320His missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474040 p.Gly12Trp missense_variant 0.14
whiB7 3568874 c.-195C>T upstream_gene_variant 0.13
Rv3236c 3612490 p.Leu209Phe missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640888 p.Thr116Ala missense_variant 0.2
alr 3840698 p.Met241Ile missense_variant 0.23
alr 3840821 c.600C>A synonymous_variant 0.17
alr 3841484 c.-64C>A upstream_gene_variant 0.13
rpoA 3877539 c.969C>T synonymous_variant 0.14
ddn 3987138 p.Gln99Lys missense_variant 0.13
clpC1 4039502 c.1203C>T synonymous_variant 0.18
panD 4043938 p.Ile115Thr missense_variant 0.17
embC 4240963 c.1101G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243412 c.180C>A synonymous_variant 0.23
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244162 c.930G>T synonymous_variant 0.22
embA 4245373 p.Pro714Arg missense_variant 0.15
embA 4245466 p.Pro745His missense_variant 0.23
embA 4245786 p.Ala852Ser missense_variant 0.22
embA 4246345 p.Arg1038His missense_variant 0.18
embB 4249737 p.Pro1075Arg missense_variant 0.11
aftB 4267042 p.Arg599Cys missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267796 c.1041G>A synonymous_variant 0.25
aftB 4267889 c.948C>A synonymous_variant 0.4
aftB 4269333 c.-497C>A upstream_gene_variant 0.22
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethA 4327551 c.-78C>A upstream_gene_variant 0.17
ethR 4327885 p.Thr113Ala missense_variant 0.14
whiB6 4338518 c.4C>A synonymous_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
gid 4408307 c.-105G>C upstream_gene_variant 0.14