TB-Profiler result

Run: SRR5535396
Summary

Run ID: SRR5535396

Sample name:

Date: 04-04-2023 10:37:29

Number of reads: 1160213

Percentage reads mapped: 98.74

Strain: lineage2.2

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
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 2289081 p.Pro54Gln missense_variant 0.13 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247431 p.Met306Ile 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 5044 c.-196C>G upstream_gene_variant 1.0
gyrB 6599 p.Glu454Lys missense_variant 0.18
gyrB 6773 p.Gly512Arg missense_variant 0.2
gyrA 7321 p.Pro7Gln missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7891 p.Leu197Gln missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9745 p.Ile815Thr missense_variant 0.13
fgd1 490662 c.-121G>T upstream_gene_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575167 c.-181G>C upstream_gene_variant 0.15
mshA 575379 p.Gly11Glu missense_variant 0.12
mshA 575390 p.Gln15Lys missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576462 p.Ala372Val missense_variant 0.22
ccsA 620101 p.Pro71Thr missense_variant 0.29
ccsA 620505 c.615G>A synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760807 p.Ala334Asp missense_variant 0.4
rpoB 760856 c.1050C>A synonymous_variant 0.2
rpoB 762528 p.Asp908His missense_variant 0.12
rpoB 762799 p.Ala998Asp missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764141 p.Ala258Ser missense_variant 0.15
rpoC 764811 p.Pro481Arg missense_variant 0.1
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765262 c.1894_1895delAA frameshift_variant 0.29
rpoC 765853 p.Lys828Asn missense_variant 0.22
rpoC 766075 c.2706C>A synonymous_variant 0.14
rpoC 766267 c.2898G>T synonymous_variant 0.25
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 777745 p.Gly246Ser missense_variant 1.0
mmpR5 778268 c.-722C>T upstream_gene_variant 0.2
mmpL5 778942 c.-462G>A upstream_gene_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800735 c.-74C>G upstream_gene_variant 0.29
fbiC 1303556 p.Pro209Gln missense_variant 0.22
fbiC 1303975 p.Ala349Pro missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 0.9
embR 1416795 p.Gly185Trp missense_variant 0.13
embR 1416872 p.Val159Ala missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476612 n.2955G>A non_coding_transcript_exon_variant 0.33
rrl 1476622 n.2965G>A non_coding_transcript_exon_variant 0.33
rpsA 1833840 p.Leu100Arg missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918625 p.Pro229Gln missense_variant 0.22
tlyA 1918703 p.Gly255Val missense_variant 0.25
ndh 2103175 c.-133G>A upstream_gene_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155563 p.Phe183Leu missense_variant 0.12
katG 2155569 c.543C>T synonymous_variant 0.12
katG 2156262 c.-151C>T upstream_gene_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.25
PPE35 2169293 c.1320T>C synonymous_variant 0.22
PPE35 2170062 p.Ala184Asp missense_variant 0.17
PPE35 2170283 c.330G>A synonymous_variant 0.18
PPE35 2170432 p.Ser61Ala missense_variant 0.18
Rv1979c 2223157 p.Gly3Ala missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223339 c.-175C>A upstream_gene_variant 0.17
pncA 2288890 p.Asn118Asp missense_variant 0.18
pncA 2289157 p.Arg29Gly missense_variant 0.2
pncA 2289541 c.-300G>T upstream_gene_variant 0.2
pncA 2289882 c.-641C>G upstream_gene_variant 0.17
kasA 2518486 p.Glu124Asp missense_variant 0.17
eis 2714231 p.Thr368Ala missense_variant 0.22
ahpC 2726078 c.-115T>C upstream_gene_variant 0.11
folC 2746170 p.Ala477Thr missense_variant 1.0
pepQ 2859427 p.Pro331His missense_variant 0.14
thyX 3067590 p.Pro119Gln missense_variant 0.22
thyA 3073906 p.Ala189Val missense_variant 1.0
thyA 3074173 p.Ser100* stop_gained 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.8
Rv3083 3448956 c.453G>A synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474796 p.His264Asn missense_variant 0.2
fprA 3475078 p.Gly358Trp missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612976 c.141C>G synonymous_variant 0.4
Rv3236c 3613236 c.-120A>G upstream_gene_variant 0.13
fbiB 3640755 c.-780C>A upstream_gene_variant 0.17
fbiB 3641937 p.Gly135Trp missense_variant 0.17
alr 3840554 c.867G>A synonymous_variant 0.15
rpoA 3877556 c.951delC frameshift_variant 0.17
rpoA 3878179 p.Ile110Asn missense_variant 0.14
ddn 3986764 c.-80C>G upstream_gene_variant 0.22
ddn 3986940 p.Asp33Asn missense_variant 0.17
clpC1 4038399 p.Gly769Val missense_variant 0.15
clpC1 4040218 p.Gly163Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244832 p.Val534Met missense_variant 0.29
embB 4246561 c.48T>A synonymous_variant 1.0
embB 4249267 c.2754C>A synonymous_variant 0.13
embB 4249702 c.3189C>G synonymous_variant 0.4
aftB 4267020 p.Pro606Gln missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268696 c.141G>T synonymous_variant 0.22
ubiA 4269022 p.Ala271Gly missense_variant 0.17
ubiA 4269593 p.Asp81Tyr missense_variant 0.15
ubiA 4269913 c.-80T>A upstream_gene_variant 0.22
ethA 4326451 c.1023A>G synonymous_variant 0.17
ethA 4326663 p.Gln271Lys missense_variant 0.2
ethR 4327096 c.-453G>A upstream_gene_variant 0.25
ethA 4327407 p.Leu23Met missense_variant 0.18
ethR 4328071 p.Leu175Ile missense_variant 0.2
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