TB-Profiler result

Run: SRR6785297
Summary

Run ID: SRR6785297

Sample name:

Date: 04-04-2023 15:43:23

Number of reads: 1934036

Percentage reads mapped: 99.58

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
pncA 2289222 p.Val7Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764669 p.Pro434Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775931 c.2550C>T synonymous_variant 0.14
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 1.0
Rv1258c 1406844 p.Ala166Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472451 n.606C>A non_coding_transcript_exon_variant 0.14
rrs 1472722 n.881delG non_coding_transcript_exon_variant 0.2
rrl 1473951 n.294G>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
fabG1 1674172 p.Met245Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155870 p.Glu81Gly missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289329 c.-88A>T upstream_gene_variant 0.14
pncA 2289775 c.-534C>A upstream_gene_variant 0.17
kasA 2517992 c.-123C>T upstream_gene_variant 0.13
folC 2746740 p.Ser287Thr missense_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449512 p.Ile337Phe missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474084 c.78C>T synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642549 p.Gln339Lys missense_variant 0.11
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 4244052 p.Asp274Asn missense_variant 0.11
embA 4244191 p.Ala320Asp missense_variant 0.12
embA 4244195 c.963C>A synonymous_variant 0.12
embA 4244788 p.Phe519Tyr missense_variant 0.12
embB 4249782 p.Ser1090* stop_gained 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269193 p.Thr214Ser missense_variant 0.11
ethR 4327438 c.-111A>G upstream_gene_variant 0.1
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