TB-Profiler result

Run: SRR6257108
Summary

Run ID: SRR6257108

Sample name:

Date: 04-04-2023 13:26:36

Number of reads: 857156

Percentage reads mapped: 100.0

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 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155734 p.Met126Ile missense_variant 0.12 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
ethA 4326707 p.Trp256* stop_gained 1.0 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
gyrB 6000 p.Pro254Gln missense_variant 0.12
gyrB 7080 p.Gly614Val missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7564 p.Gly88Val missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491286 c.504G>T synonymous_variant 0.12
fgd1 491400 p.Lys206Asn missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575837 p.Leu164Met missense_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
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
mmpL5 777283 p.Leu400Met missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781362 c.-198G>T upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801111 p.Leu101Phe missense_variant 0.11
fbiC 1303113 p.Ser61Arg missense_variant 0.15
fbiC 1303160 p.Gly77Val missense_variant 0.11
fbiC 1303903 p.Leu325Met missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407374 c.-34T>C upstream_gene_variant 0.14
embR 1417012 c.336G>T synonymous_variant 0.12
atpE 1461096 p.Ala18Thr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472543 n.698T>C non_coding_transcript_exon_variant 0.11
inhA 1673562 c.-640G>A upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102583 p.Ala154Ser missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170105 p.Leu170Ile missense_variant 0.17
PPE35 2170510 p.Ala35Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289811 c.-570C>A upstream_gene_variant 0.11
pncA 2289936 c.-695T>C upstream_gene_variant 0.11
ribD 2986994 c.156C>A synonymous_variant 0.11
ribD 2987285 c.447C>A synonymous_variant 0.25
thyA 3074657 c.-186C>G upstream_gene_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612029 p.Ala363Val missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612818 p.Asn100Ser missense_variant 0.17
fbiA 3640480 c.-63C>T upstream_gene_variant 0.15
fbiA 3641333 p.Gly264Val missense_variant 0.12
rpoA 3878630 c.-123G>C upstream_gene_variant 0.4
ddn 3986653 c.-191G>T upstream_gene_variant 0.2
clpC1 4040889 c.-185C>A upstream_gene_variant 0.12
embC 4240515 p.Val218Ala missense_variant 0.17
embA 4242406 c.-827A>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243843 p.Lys204Arg missense_variant 0.17
embA 4243861 p.Gly210Val missense_variant 0.17
embA 4245492 p.Pro754Thr missense_variant 0.12
embB 4249339 c.2826T>C synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268801 c.36G>A synonymous_variant 0.13
ubiA 4268936 p.Ala300Ser missense_variant 0.25
ubiA 4269981 c.-148G>A upstream_gene_variant 0.13
ethR 4327891 p.Gly115Trp missense_variant 0.13
whiB6 4338371 p.Thr51Pro 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