TB-Profiler result

Run: SRR11972312
Summary

Run ID: SRR11972312

Sample name:

Date: 03-04-2023 05:36:42

Number of reads: 1318484

Percentage reads mapped: 99.37

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 2288887 p.Trp119Gly missense_variant 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 5766 p.Asp176Gly missense_variant 0.11
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
mshA 576472 c.1125C>A synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761773 p.His656Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763192 p.Val1129Ala missense_variant 0.13
rpoC 764237 p.Leu290Phe missense_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765233 p.Ala622Thr missense_variant 0.13
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 776256 p.Ala742Asp missense_variant 0.22
mmpR5 778007 c.-983G>C upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303113 c.183C>T synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834678 c.1137C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101766 p.Arg426His missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155810 p.Leu101Pro missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170372 p.Thr81Ala missense_variant 0.11
PPE35 2170385 c.228G>T synonymous_variant 0.16
PPE35 2170392 p.Gly74Ala missense_variant 0.17
PPE35 2170400 c.213G>C synonymous_variant 0.19
PPE35 2170412 c.201G>A synonymous_variant 0.12
PPE35 2170415 c.198A>G synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715449 c.-117G>C upstream_gene_variant 0.13
folC 2746215 p.Ser462Thr missense_variant 0.29
folC 2746257 p.Asp448His missense_variant 0.22
Rv2752c 3065193 c.998delT frameshift_variant 1.0
thyA 3074512 c.-41G>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448319 c.-185C>G upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474024 c.18C>T synonymous_variant 0.14
fprA 3475101 c.1099dupG frameshift_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039151 c.1554C>A synonymous_variant 0.25
clpC1 4039730 c.975C>G synonymous_variant 0.18
embC 4239962 p.Val34Met missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242775 c.-458G>A upstream_gene_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245728 p.Leu832Phe missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246896 p.Arg128His missense_variant 0.5
embB 4246994 p.Phe161Leu missense_variant 0.18
embB 4247717 p.Leu402Val missense_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4268942 p.Ala298Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.97
gid 4408206 c.-4C>A upstream_gene_variant 0.11