TB-Profiler result

Run: SRR11972229
Summary

Run ID: SRR11972229

Sample name:

Date: 03-04-2023 05:32:44

Number of reads: 268133

Percentage reads mapped: 99.41

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 2155423 p.Val230Ala missense_variant 0.2 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
pncA 2288537 c.-744_*143del transcript_ablation 1.0 pyrazinamide
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 5348 p.Thr37Ala missense_variant 0.33
gyrA 7057 c.-245C>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8413 p.Asp371Gly missense_variant 0.12
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 760041 p.Gly79Ser missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763042 p.Leu1079Pro missense_variant 0.13
rpoC 763685 c.317delA frameshift_variant 0.12
rpoC 764918 p.Val517Leu missense_variant 1.0
rpoC 765402 p.Pro678Leu missense_variant 0.29
mmpL5 775588 c.2893T>A stop_lost&splice_region_variant 0.18
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 777256 p.Pro409Ser missense_variant 0.18
mmpR5 778430 c.-560C>T upstream_gene_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302856 c.-75T>C upstream_gene_variant 0.17
fbiC 1303590 c.660A>G synonymous_variant 0.29
fbiC 1304840 p.Glu637Gly missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473602 n.-56G>A upstream_gene_variant 0.18
rrl 1474726 n.1069A>G non_coding_transcript_exon_variant 0.1
rrl 1475640 n.1983G>A non_coding_transcript_exon_variant 0.15
rrl 1475782 n.2125T>C non_coding_transcript_exon_variant 0.13
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.2
rpsA 1834032 p.Tyr164Cys missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917859 c.-81A>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918125 p.Trp62Cys missense_variant 0.13
ndh 2101794 p.Trp417Arg missense_variant 0.12
katG 2154058 p.Gly685Asp missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154789 c.1323G>A synonymous_variant 0.15
PPE35 2167884 p.Gly910Asp missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168265 p.Gly783Glu missense_variant 0.33
PPE35 2169065 c.1548G>A synonymous_variant 0.18
Rv1979c 2221862 p.Arg435Cys missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290165 c.-924C>T upstream_gene_variant 0.4
kasA 2518375 c.263delA frameshift_variant 0.15
kasA 2518696 c.582C>A synonymous_variant 0.33
kasA 2519361 p.Tyr416Ser missense_variant 0.22
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2747327 p.Arg91Gln missense_variant 0.33
pepQ 2859653 p.Ala256Ser missense_variant 0.22
pepQ 2859670 p.Tyr250Ser missense_variant 0.3
pepQ 2859762 p.Lys219Asn missense_variant 0.22
pepQ 2860149 c.270C>G synonymous_variant 0.22
Rv2752c 3064950 c.1242C>A synonymous_variant 0.22
Rv2752c 3065767 p.Glu142Val missense_variant 0.17
thyA 3074205 c.267A>G synonymous_variant 0.17
thyA 3074232 p.Trp80* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087403 p.Thr195Met missense_variant 0.29
ald 3087483 p.Ala222Thr missense_variant 0.18
Rv3083 3448605 c.102C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474579 c.573C>T synonymous_variant 0.25
Rv3236c 3612396 p.Ala241Thr missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641610 p.Gly26Ser missense_variant 0.25
fbiB 3642700 p.Ala389Val missense_variant 0.33
alr 3841546 c.-126C>A upstream_gene_variant 0.2
rpoA 3877853 p.Phe219Leu missense_variant 0.25
clpC1 4039498 p.Ile403Val missense_variant 0.18
panD 4043993 p.Arg97Gly missense_variant 0.22
panD 4044241 p.Thr14Lys missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242787 c.-446G>T upstream_gene_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245438 p.Ala736Thr missense_variant 0.29
embB 4246521 p.Gln3Arg missense_variant 0.29
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267138 p.Gln567* stop_gained 0.14
aftB 4267274 c.1563G>T synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326342 p.Pro378Thr missense_variant 0.17
ethR 4327447 c.-102G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407575 p.Gln210Lys missense_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0