TB-Profiler result

Run: ERR4831894
Summary

Run ID: ERR4831894

Sample name:

Date: 01-04-2023 21:11:33

Number of reads: 1050431

Percentage reads mapped: 87.67

Strain: lineage2.2.1.1

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.99
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
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288943 c.298dupA frameshift_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8782 p.Arg494Pro missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.4
rpoB 761534 c.1728G>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.12
rrl 1475284 n.1627C>G non_coding_transcript_exon_variant 1.0
rrl 1475385 n.1728G>T non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.3
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.23
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.23
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.3
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.33
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.38
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.43
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476756 n.3099G>T non_coding_transcript_exon_variant 0.25
inhA 1674045 c.-157G>A upstream_gene_variant 0.12
rpsA 1833775 p.Glu78Asp missense_variant 0.4
rpsA 1833791 p.Asp84Tyr missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 0.89
rpsA 1834319 p.Val260Ile missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101906 c.1137G>A synonymous_variant 0.17
ndh 2101976 p.Pro356Leu missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155903 p.Thr70Ile missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169386 c.1227C>T synonymous_variant 0.12
PPE35 2169605 p.Asn336Thr missense_variant 0.11
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519136 p.Ser341Tyr missense_variant 0.14
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726513 c.321C>A synonymous_variant 0.17
thyA 3074648 c.-177T>G upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612041 p.Val359Ala missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642237 p.Pro235Thr missense_variant 0.12
rpoA 3877949 p.Thr187Pro missense_variant 1.0
rpoA 3878384 p.Leu42Met missense_variant 0.12
clpC1 4040702 c.3G>T start_lost 0.15
embC 4241609 p.Pro583Thr missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245431 p.Cys733Trp missense_variant 0.15
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249674 p.Ser1054Phe missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269313 p.Lys174Thr missense_variant 1.0
ubiA 4269533 p.Leu101Met missense_variant 0.13
ethA 4326200 p.Asp425Gly missense_variant 0.12
ethA 4327440 p.Ala12Pro missense_variant 0.18
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