TB-Profiler result

Run: SRR11972421
Summary

Run ID: SRR11972421

Sample name:

Date: 03-04-2023 05:41:26

Number of reads: 508232

Percentage reads mapped: 99.32

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761158 p.Ala451Val missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6839 p.Asp534Asn missense_variant 0.15
gyrA 7252 c.-50G>A upstream_gene_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 490751 c.-32T>G upstream_gene_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.43
rpoB 759940 p.Pro45Arg missense_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 0.14
rpoB 761111 c.1305C>T synonymous_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 776923 p.Ala520Thr missense_variant 0.13
mmpR5 779263 p.Tyr92Asp missense_variant 0.25
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472602 n.757A>T non_coding_transcript_exon_variant 0.2
rrl 1474964 n.1307T>C non_coding_transcript_exon_variant 0.4
fabG1 1673302 c.-138T>C upstream_gene_variant 0.18
fabG1 1673657 p.Thr73Met missense_variant 0.15
inhA 1674354 c.153C>T synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918503 c.564G>A synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155454 c.658C>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289801 c.-560C>T upstream_gene_variant 0.13
pncA 2289909 c.-668G>A upstream_gene_variant 0.15
folC 2747617 c.-19C>A upstream_gene_variant 0.12
pepQ 2859308 p.Ile371Val missense_variant 0.15
Rv2752c 3064946 p.Pro416Ser missense_variant 0.13
Rv2752c 3065129 c.1063C>T synonymous_variant 1.0
Rv2752c 3066100 p.Met31Lys missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339520 p.His135Tyr missense_variant 0.17
fbiD 3339574 p.Ala153Ser missense_variant 0.29
Rv3083 3448407 c.-97A>T upstream_gene_variant 0.14
Rv3083 3449382 p.Trp293Cys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612097 c.1020C>A synonymous_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642630 p.Thr366Ser missense_variant 0.13
alr 3840664 p.Pro253Thr missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.23
clpC1 4039161 p.His515Arg missense_variant 0.12
clpC1 4039169 p.Glu512Asp missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.13
panD 4044339 c.-58C>T upstream_gene_variant 0.22
embA 4242304 c.-929G>T upstream_gene_variant 0.13
embC 4242324 p.Gly821Val missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407528 c.675A>T stop_lost&splice_region_variant 0.33
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0