TB-Profiler result

Run: ERR5866375
Summary

Run ID: ERR5866375

Sample name:

Date: 02-04-2023 00:39:08

Number of reads: 772953

Percentage reads mapped: 97.36

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 0.96
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.95
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 0.76 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247730 p.Gly406Ala 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 5506 c.267C>T synonymous_variant 0.12
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 575596 c.249C>A synonymous_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619945 p.Thr19Ala missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760841 c.1035T>C synonymous_variant 0.18
rpoB 761531 c.1726delT frameshift_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764418 p.Arg350His missense_variant 0.11
rpoC 765150 p.Gly594Val missense_variant 0.11
rpoC 766868 p.Ile1167Val missense_variant 0.16
rpoC 767280 p.Ala1304Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778401 p.Met27Thr missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304800 p.Arg624Trp missense_variant 0.17
Rv1258c 1406517 p.Ala275Glu missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416734 c.613delG frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475233 n.1576C>T non_coding_transcript_exon_variant 0.13
rrl 1476469 n.2812G>T non_coding_transcript_exon_variant 0.17
inhA 1674201 c.-1C>A upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918018 p.Ile27Val missense_variant 1.0
ndh 2103067 c.-25G>T upstream_gene_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 0.89
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289071 p.His57Gln missense_variant 1.0
pncA 2289254 c.-13G>A upstream_gene_variant 0.18
pncA 2290168 c.-927G>A upstream_gene_variant 0.2
kasA 2518513 c.399C>T synonymous_variant 0.29
eis 2715332 p.Val1Leu missense_variant 1.0
Rv2752c 3064779 c.1413C>T synonymous_variant 0.17
Rv2752c 3065518 p.Leu225Pro missense_variant 1.0
Rv2752c 3065770 p.Cys141Phe missense_variant 0.18
Rv2752c 3067092 c.-901C>A upstream_gene_variant 0.12
thyX 3067194 c.752G>T stop_lost&splice_region_variant 0.12
thyX 3067496 c.450G>T synonymous_variant 0.18
thyA 3074638 c.-167C>G upstream_gene_variant 0.13
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087856 p.His346Arg missense_variant 0.12
fbiD 3339546 c.429G>A synonymous_variant 0.17
Rv3083 3448616 p.Arg38Leu missense_variant 0.17
Rv3083 3448641 p.Asp46Glu missense_variant 0.17
Rv3083 3448764 p.Asp87Glu missense_variant 0.11
Rv3083 3449645 p.Ala381Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474067 p.Ser21Pro missense_variant 0.22
fprA 3474122 p.Leu39Gln missense_variant 0.17
fprA 3475351 c.1346delA frameshift_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640638 c.-897T>C upstream_gene_variant 0.17
fbiB 3641739 c.208delA frameshift_variant 0.15
alr 3841525 c.-105G>T upstream_gene_variant 0.18
rpoA 3877969 p.Ala180Gly missense_variant 1.0
clpC1 4039067 c.1638G>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242865 p.Tyr1001* stop_gained 0.13
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244255 c.1023T>A synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269303 c.530delT frameshift_variant 0.17
ethA 4326155 p.Leu440Pro missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407927 p.Glu92Asp missense_variant 1.0