TB-Profiler result

Run: ERR4831746
Summary

Run ID: ERR4831746

Sample name:

Date: 01-04-2023 21:05:49

Number of reads: 1548367

Percentage reads mapped: 98.86

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 0.99
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 761095 p.Leu430Pro missense_variant 0.92 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.9 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9524 c.2223G>A synonymous_variant 1.0
fgd1 491313 c.531C>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575975 p.Ala210Ser missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759724 c.-83A>G upstream_gene_variant 1.0
rpoB 761147 c.1341C>T synonymous_variant 0.17
rpoB 761150 c.1344A>T synonymous_variant 0.17
rpoB 761165 c.1359G>C synonymous_variant 0.17
rpoB 761171 c.1365C>T synonymous_variant 0.2
rpoB 761178 p.Ser458Thr missense_variant 0.12
rpoB 761186 p.Glu460Asp missense_variant 0.17
rpoB 761189 c.1383T>C synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761198 c.1392G>C synonymous_variant 0.15
rpoB 761219 c.1413G>C synonymous_variant 0.12
rpoB 761234 c.1428G>C synonymous_variant 0.12
rpoB 762165 p.Gly787Arg missense_variant 0.11
rpoB 762493 p.Glu896Gly missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763880 p.Glu171* stop_gained 0.12
rpoC 766344 p.Gly992Asp missense_variant 0.13
rpoC 766996 c.3627C>T synonymous_variant 0.29
rpoC 767002 c.3633G>C synonymous_variant 0.25
rpoC 767008 c.3639G>A synonymous_variant 0.22
rpoC 767023 c.3654C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777311 c.1170C>A synonymous_variant 0.17
mmpR5 779181 c.198delG frameshift_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801056 p.Glu83Gly missense_variant 0.11
fbiC 1303960 p.Arg344Trp missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474044 n.387C>A non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.22
rrl 1475368 n.1711C>G non_coding_transcript_exon_variant 1.0
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101700 p.Leu448Arg missense_variant 0.14
ndh 2103144 c.-102T>C upstream_gene_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170050 p.Ala188Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 1.0
eis 2714739 p.Asp198Glu missense_variant 0.2
eis 2715487 c.-155G>T upstream_gene_variant 0.12
folC 2746560 c.1038delC frameshift_variant 0.25
folC 2746683 p.Leu306Ile missense_variant 0.12
folC 2746823 c.770_775dupCCCGGG conservative_inframe_insertion 0.17
pepQ 2859445 c.973delG frameshift_variant 0.13
pepQ 2860261 p.Val53Glu missense_variant 0.12
Rv2752c 3065594 c.598C>T synonymous_variant 1.0
thyX 3067251 p.Val232Ala missense_variant 0.13
thyX 3067401 p.Arg182His missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475318 p.Gly438Trp missense_variant 0.11
Rv3236c 3612546 c.569_570delCC frameshift_variant 0.25
Rv3236c 3612591 p.Gly176Cys missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642238 p.Pro235Leu missense_variant 0.13
fbiB 3642634 p.Asp367Gly missense_variant 0.22
embC 4240651 c.789G>T synonymous_variant 0.18
embC 4241830 p.Lys656Asn missense_variant 0.11
embA 4242455 c.-778C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244653 p.Gln474Arg missense_variant 0.11
embA 4245660 p.Ala810Thr missense_variant 0.12
embB 4247847 p.Gln445Arg missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268610 p.Pro76Leu missense_variant 0.14
ubiA 4269719 p.Ala39Ser missense_variant 0.12
ubiA 4269722 p.Ala38Ser missense_variant 0.12
ubiA 4269731 p.Ala35Ser missense_variant 0.14
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338238 p.Leu95Arg missense_variant 0.9
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