TB-Profiler result

Run: SRR11972160
Summary

Run ID: SRR11972160

Sample name:

Date: 03-04-2023 05:30:14

Number of reads: 734602

Percentage reads mapped: 99.07

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 761140 p.His445Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6144 p.His302Arg missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7530 p.Val77Phe missense_variant 0.15
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 619795 c.-96C>A upstream_gene_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760592 c.786C>T synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763815 p.Ser149Tyr missense_variant 0.17
rpoC 764058 p.Ala230Val missense_variant 1.0
rpoC 766165 p.Glu932Asp missense_variant 0.12
rpoC 766742 p.Gln1125Lys missense_variant 0.14
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 777173 c.1308C>T synonymous_variant 0.22
mmpL5 777176 p.Glu435Asp missense_variant 0.22
mmpL5 777476 c.1005C>A synonymous_variant 0.25
mmpL5 778115 p.His122Gln missense_variant 0.15
mmpS5 778730 p.Glu59Gly missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781381 c.-179C>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.18
Rv1258c 1407157 p.Ala62Thr missense_variant 0.13
embR 1416984 p.Gly122Ser missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>T non_coding_transcript_exon_variant 0.15
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.34
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.21
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.23
fabG1 1673349 c.-91G>C upstream_gene_variant 0.27
fabG1 1673357 c.-83G>A upstream_gene_variant 0.19
fabG1 1673359 c.-81T>C upstream_gene_variant 0.24
fabG1 1673361 c.-79C>G upstream_gene_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834210 c.669C>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918194 c.255C>A synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154740 p.Leu458Ile missense_variant 0.2
PPE35 2167746 p.Thr956Asn missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.21
PPE35 2170147 p.Ser156Ala missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518700 p.Gly196Cys missense_variant 0.22
folC 2746895 p.Gly235Val missense_variant 0.14
folC 2747437 p.Met54Ile missense_variant 1.0
pepQ 2859384 c.1035T>G synonymous_variant 0.12
ribD 2986719 c.-120G>A upstream_gene_variant 0.12
ribD 2987088 p.Gly84Ser missense_variant 0.29
ribD 2987500 p.Gly221Asp missense_variant 0.2
Rv2752c 3064963 p.Ala410Val missense_variant 0.14
Rv2752c 3065664 p.Leu176Phe missense_variant 0.14
thyX 3068077 c.-132C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339720 c.603C>T synonymous_variant 0.2
Rv3083 3448785 c.282C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474335 p.Arg110His missense_variant 0.18
fprA 3474391 p.Val129Phe missense_variant 0.22
fprA 3474766 p.Gly254Ser missense_variant 0.29
Rv3236c 3612267 p.Pro284Thr missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641077 p.Gln179Lys missense_variant 0.14
fbiB 3641502 c.-33T>A upstream_gene_variant 0.17
fbiB 3641557 p.Ser8Tyr missense_variant 0.15
fbiB 3641596 p.Pro21Leu missense_variant 0.12
fbiB 3642792 p.Pro420Ser missense_variant 0.13
fbiB 3642855 p.Ala441Thr missense_variant 0.15
clpC1 4038421 p.Arg762Ser missense_variant 0.22
clpC1 4038898 p.Gly603Ser missense_variant 0.18
clpC1 4039654 p.Thr351Ser missense_variant 0.12
clpC1 4040126 c.579C>A synonymous_variant 0.14
embC 4240648 c.786C>T synonymous_variant 0.33
embC 4240655 p.Ala265Pro missense_variant 0.4
embC 4240806 p.Arg315Leu missense_variant 0.22
embC 4241492 p.Leu544Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245417 p.Gly729Trp missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.8
embB 4246556 p.Ala15Pro missense_variant 0.8
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268130 p.Val236Asp missense_variant 0.12
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