TB-Profiler result

Run: ERR2515539
Summary

Run ID: ERR2515539

Sample name:

Date: 31-03-2023 20:59:13

Number of reads: 523851

Percentage reads mapped: 98.9

Strain: lineage2.2.1.1

Drug-resistance: RR-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 1.0
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 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 761139 p.His445Asp missense_variant 1.0 rifampicin
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 7321 p.Pro7Gln missense_variant 0.12
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576064 p.His239Gln missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763692 p.Lys108Arg missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775904 p.Lys859Asn missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777357 p.Arg375Leu missense_variant 0.12
mmpL5 777368 c.1113G>A synonymous_variant 0.12
mmpS5 779551 c.-646A>G upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800963 c.157delG frameshift_variant 0.12
rplC 801113 p.Thr102Asn missense_variant 0.13
fbiC 1304658 c.1728C>A synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416995 p.Glu118Val missense_variant 0.17
embR 1417116 p.Asn78Asp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917851 c.-89C>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155844 p.Trp90Arg missense_variant 0.14
katG 2155920 c.192T>C synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.29
PPE35 2170403 c.210C>A synonymous_variant 0.2
Rv1979c 2223014 p.Tyr51Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289876 c.-635G>C upstream_gene_variant 0.11
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715067 p.Pro89Leu missense_variant 0.14
eis 2715440 c.-108A>G upstream_gene_variant 0.14
ahpC 2726033 c.-160C>T upstream_gene_variant 0.12
folC 2747754 c.-156C>T upstream_gene_variant 0.11
pepQ 2859992 p.Leu143Met missense_variant 0.2
pepQ 2860106 p.Asp105Tyr missense_variant 0.14
Rv2752c 3067109 c.-918T>A upstream_gene_variant 0.13
thyX 3067722 p.His75Leu missense_variant 0.15
thyA 3074467 p.Thr2Arg missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339238 p.Ala41Thr missense_variant 0.12
fbiD 3339270 c.153G>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474024 c.18C>T synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840968 c.453G>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243235 c.7delC frameshift_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244611 p.Ala460Val missense_variant 0.11
embA 4244940 p.Trp570Arg missense_variant 0.4
embB 4247094 p.Gly194Glu missense_variant 0.12
embB 4247769 p.Ile419Asn missense_variant 0.11
embB 4248039 p.Arg509His missense_variant 0.14
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249524 p.Asn1004Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
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