TB-Profiler result

Run: SRR11972157
Summary

Run ID: SRR11972157

Sample name:

Date: 03-04-2023 05:30:15

Number of reads: 466610

Percentage reads mapped: 99.15

Strain: lineage2.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn 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 6545 p.Gly436Cys missense_variant 0.18
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
rpoB 760816 p.Glu337Gly missense_variant 0.5
rpoB 761420 c.1614C>T synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763082 c.-288C>T upstream_gene_variant 0.15
rpoC 764058 p.Ala230Val missense_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765096 p.Met576Lys missense_variant 0.17
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 777608 c.873C>T synonymous_variant 0.33
mmpL5 778972 c.-492G>A upstream_gene_variant 0.22
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 1472193 n.348A>G non_coding_transcript_exon_variant 0.36
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.5
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.44
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.29
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.17
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.26
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.29
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.32
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.22
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.22
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.24
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.21
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.33
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.4
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.4
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.4
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.4
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.4
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.4
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.4
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.4
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.29
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
fabG1 1673526 c.87_88insT frameshift_variant 0.22
inhA 1674546 p.Asp115Glu missense_variant 0.29
rpsA 1833736 c.195C>T synonymous_variant 0.15
rpsA 1833738 p.Arg66His missense_variant 0.17
rpsA 1833832 c.291G>A synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918171 p.Ala78Thr missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.19
PPE35 2167868 c.2745A>C synonymous_variant 0.19
PPE35 2167878 p.Ser912Asn missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169351 p.Ala421Gly missense_variant 0.12
PPE35 2169363 p.Ile417Thr missense_variant 0.12
PPE35 2169884 c.729T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.57
PPE35 2170288 p.Leu109Val missense_variant 0.12
PPE35 2170308 p.Leu102Ala missense_variant 0.12
PPE35 2170313 c.300G>C synonymous_variant 0.13
PPE35 2170403 c.210C>G synonymous_variant 0.18
PPE35 2170406 c.207A>G synonymous_variant 0.18
Rv1979c 2222968 p.Ala66Val missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.2
folC 2746180 c.1419C>A synonymous_variant 0.29
folC 2747437 p.Met54Ile missense_variant 1.0
ribD 2986950 p.Gly38Ser missense_variant 0.17
ribD 2987587 p.Tyr250Cys missense_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087309 p.Pro164Ala missense_variant 0.12
ald 3087369 p.Ala184Pro missense_variant 0.14
fprA 3473952 c.-55C>T upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642427 p.Val298Ala missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4039508 c.1197G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244575 p.Ala448Val missense_variant 0.17
embB 4246052 c.-462C>A upstream_gene_variant 0.33
embB 4246824 p.Lys104Arg missense_variant 0.11
embB 4247461 p.Met316Ile missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327087 c.-462G>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338605 c.-84C>T upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0