TB-Profiler result

Run: ERR027465
Summary

Run ID: ERR027465

Sample name:

Date: 31-03-2023 08:21:35

Number of reads: 3005871

Percentage reads mapped: 99.79

Strain: lineage4.9;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 0.29
lineage4 Euro-American LAM;T;S;X;H None 0.65
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.36
lineage4.9 Euro-American (H37Rv-like) T1 None 0.58
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.43
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 0.33 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.41 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.57 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid
embB 4247429 p.Met306Val missense_variant 0.19 ethambutol
ethA 4326463 c.1010delT frameshift_variant 0.32 ethionamide, ethionamide
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 0.33
gyrA 7585 p.Ser95Thr missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 0.42
fgd1 491742 c.960T>C synonymous_variant 0.23
mshA 575907 p.Ala187Val missense_variant 0.44
ccsA 620625 p.Ile245Met missense_variant 0.41
rpoC 763031 c.-339T>C upstream_gene_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 0.32
mmpL5 776100 p.Thr794Ile missense_variant 0.48
mmpL5 776182 p.Asp767Asn missense_variant 0.34
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 0.27
Rv1258c 1406760 c.580_581insC frameshift_variant 0.25
Rv1258c 1407240 p.Val34Gly missense_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 0.3
rrl 1474241 n.584G>C non_coding_transcript_exon_variant 0.23
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.36
rpsA 1834177 c.636A>C synonymous_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 0.31
katG 2154724 p.Arg463Leu missense_variant 0.55
PPE35 2167926 p.Leu896Ser missense_variant 0.4
PPE35 2169320 p.Leu431Phe missense_variant 0.31
PPE35 2169379 p.Phe412Val missense_variant 0.39
PPE35 2169866 c.747G>C synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.41
folC 2747263 c.336C>A synonymous_variant 0.27
pepQ 2859381 c.1038C>G synonymous_variant 0.35
thyX 3067995 c.-50A>C upstream_gene_variant 0.19
ald 3086731 c.-89A>G upstream_gene_variant 0.39
ald 3086788 c.-32T>C upstream_gene_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.45
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039932 p.Gly258Val missense_variant 0.35
embC 4239842 c.-21C>A upstream_gene_variant 0.35
embC 4242822 p.Val987Gly missense_variant 0.33
embA 4243346 c.114A>G synonymous_variant 0.25
embA 4243460 c.228C>T synonymous_variant 0.29
whiB6 4338371 p.Thr51Pro missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 0.41
gid 4407588 c.615A>G synonymous_variant 0.32