TB-Profiler result

Run: ERR5864266
Summary

Run ID: ERR5864266

Sample name:

Date: 01-04-2023 23:14:04

Number of reads: 511217

Percentage reads mapped: 99.54

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 2154246 c.1864_1865delCC frameshift_variant 0.2 isoniazid
katG 2154742 p.Ser457Ile missense_variant 0.14 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155532 c.579delC frameshift_variant 0.1 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4324388 c.-2186_*1615del transcript_ablation 1.0 ethionamide
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 5078 c.-162C>A upstream_gene_variant 0.2
gyrB 5300 p.Glu21* stop_gained 0.18
gyrB 5557 c.318C>A synonymous_variant 0.22
gyrB 6148 c.909C>A synonymous_variant 0.17
gyrB 6350 p.Thr371Ala missense_variant 0.1
gyrB 7079 p.Gly614Cys missense_variant 0.22
gyrB 7087 p.Met616Ile missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7507 p.Ser69Asn missense_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8122 p.Leu274Ser missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491093 p.Gly104Val missense_variant 0.13
fgd1 491427 c.645C>A synonymous_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575282 c.-66C>A upstream_gene_variant 0.22
mshA 575724 p.Pro126His missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620356 p.Leu156Ile missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759751 c.-56G>T upstream_gene_variant 0.17
rpoB 759818 c.12C>G synonymous_variant 0.1
rpoB 760791 p.Glu329* stop_gained 0.18
rpoB 762684 p.Ala960Thr missense_variant 0.13
rpoB 762994 p.Gly1063Val missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764618 c.1249C>T synonymous_variant 0.14
rpoC 764784 p.Ala472Asp missense_variant 0.13
rpoC 764908 p.Glu513Asp missense_variant 0.18
rpoC 765148 c.1783delG frameshift_variant 0.14
rpoC 766150 c.2781C>A synonymous_variant 0.18
rpoC 766300 c.2931C>A synonymous_variant 0.29
rpoC 767016 p.Ala1216Asp missense_variant 0.17
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 777515 p.Phe322Leu missense_variant 0.23
mmpL5 778219 p.Asp88Tyr missense_variant 0.18
mmpR5 779375 p.Pro129Gln missense_variant 0.19
mmpR5 779393 p.Arg135Leu missense_variant 0.14
mmpS5 779534 c.-629C>A upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303848 p.Phe306Leu missense_variant 0.16
fbiC 1304118 c.1188C>A synonymous_variant 0.18
fbiC 1304130 p.Gln400His missense_variant 0.17
fbiC 1304400 c.1470C>A synonymous_variant 0.18
fbiC 1304761 p.Val611Ile missense_variant 0.22
fbiC 1305121 p.Asp731Tyr missense_variant 0.17
fbiC 1305424 p.Glu832* stop_gained 0.27
fbiC 1305440 p.Ala837Asp missense_variant 0.15
Rv1258c 1406460 p.Ala294Glu missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407317 c.24G>T synonymous_variant 0.15
Rv1258c 1407520 c.-180A>G upstream_gene_variant 0.17
embR 1416517 c.831C>A synonymous_variant 0.25
embR 1416742 c.606C>A synonymous_variant 0.15
embR 1416865 c.483C>A synonymous_variant 0.14
embR 1417127 p.Ser74Tyr missense_variant 0.2
embR 1417147 c.201C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472825 n.980G>T non_coding_transcript_exon_variant 0.2
rrs 1472842 n.997G>T non_coding_transcript_exon_variant 0.17
rrl 1473828 n.171G>T non_coding_transcript_exon_variant 0.18
rrl 1473877 n.220G>T non_coding_transcript_exon_variant 0.17
rrl 1474172 n.515C>A non_coding_transcript_exon_variant 0.14
rrl 1474378 n.721G>T non_coding_transcript_exon_variant 0.15
fabG1 1673277 c.-163C>A upstream_gene_variant 0.15
fabG1 1673303 c.-137C>A upstream_gene_variant 0.18
inhA 1674576 c.375T>C synonymous_variant 0.14
inhA 1674728 p.Ala176Glu missense_variant 0.2
rpsA 1833589 p.Ile16Met missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834636 c.1095C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918406 p.Ser156* stop_gained 0.23
katG 2154153 c.1959G>T synonymous_variant 0.22
katG 2154518 p.Ala532Ser missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156487 c.-376G>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168777 c.1834_1835delAC frameshift_variant 0.14
PPE35 2170093 p.Leu174Ile missense_variant 0.17
PPE35 2170325 c.287delA frameshift_variant 0.18
PPE35 2170681 c.-69G>T upstream_gene_variant 0.2
Rv1979c 2223194 c.-30G>T upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289239 c.3G>T start_lost 0.14
pncA 2289465 c.-224G>T upstream_gene_variant 0.22
pncA 2289581 c.-340G>A upstream_gene_variant 0.15
pncA 2289769 c.-528G>T upstream_gene_variant 0.18
pncA 2289824 c.-584delA upstream_gene_variant 0.18
pncA 2290142 c.-901G>T upstream_gene_variant 0.22
kasA 2518318 c.204C>A synonymous_variant 0.3
kasA 2518531 c.417G>T synonymous_variant 0.29
kasA 2518600 c.486C>A synonymous_variant 0.25
kasA 2518861 p.Glu249Asp missense_variant 0.17
kasA 2519072 p.Ala320Ser missense_variant 0.27
kasA 2519242 c.1128C>A synonymous_variant 0.2
eis 2714325 c.1008C>A synonymous_variant 0.13
eis 2715174 c.159C>A synonymous_variant 0.18
ahpC 2726656 p.Gly155Val missense_variant 0.17
ahpC 2726777 c.585C>A synonymous_variant 0.18
folC 2746247 p.Ala451Asp missense_variant 0.17
folC 2746891 c.706_707delCG frameshift_variant 0.14
folC 2746990 p.Asp203Glu missense_variant 0.22
pepQ 2859829 p.Gly197Val missense_variant 0.17
pepQ 2860095 p.Asp108Glu missense_variant 0.15
ribD 2987401 p.Arg188Leu missense_variant 0.15
Rv2752c 3064553 p.Arg547Cys missense_variant 0.29
Rv2752c 3064820 p.Gly458Arg missense_variant 0.1
Rv2752c 3064852 p.Met447Thr missense_variant 0.1
Rv2752c 3065156 p.Glu346* stop_gained 0.2
thyX 3067615 p.Glu111* stop_gained 0.29
thyX 3067996 c.-51G>T upstream_gene_variant 0.2
thyX 3068032 c.-87G>T upstream_gene_variant 0.2
thyX 3068118 c.-173C>A upstream_gene_variant 0.22
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086993 c.174C>A synonymous_variant 0.18
fbiD 3338921 c.-197C>T upstream_gene_variant 0.17
fbiD 3339058 c.-60G>T upstream_gene_variant 0.2
Rv3083 3449327 p.Arg275Leu missense_variant 0.15
Rv3083 3449364 c.861C>A synonymous_variant 0.18
fprA 3473841 c.-166T>C upstream_gene_variant 0.12
fprA 3473848 c.-159C>A upstream_gene_variant 0.17
fprA 3473877 c.-130G>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474277 p.Gly91Cys missense_variant 0.15
Rv3236c 3612237 p.Ala294Ser missense_variant 0.2
Rv3236c 3612455 p.Arg221Pro missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613306 c.-190G>T upstream_gene_variant 0.18
fbiA 3640594 p.Gly18Trp missense_variant 0.5
fbiA 3640919 p.Ser126* stop_gained 0.25
fbiA 3641236 p.Ala232Ser missense_variant 0.13
fbiA 3641242 c.703delG frameshift_variant 0.11
fbiB 3641816 c.282C>A synonymous_variant 0.18
fbiB 3642030 p.Gly166Cys missense_variant 0.18
fbiB 3642561 p.Asp343Tyr missense_variant 0.25
fbiB 3642803 c.1269C>A synonymous_variant 0.2
alr 3840224 c.1197C>A synonymous_variant 0.5
alr 3841580 c.-160C>A upstream_gene_variant 0.22
alr 3841593 c.-173C>A upstream_gene_variant 0.3
alr 3841614 c.-194C>A upstream_gene_variant 0.2
rpoA 3877956 p.Glu184Asp missense_variant 1.0
rpoA 3878398 p.Ser37* stop_gained 0.22
rpoA 3878439 c.69C>A synonymous_variant 0.18
ddn 3986972 c.130delA frameshift_variant 0.18
ddn 3986983 p.Ala47Glu missense_variant 0.2
ddn 3987011 c.168C>A synonymous_variant 0.15
ddn 3987106 p.Trp88Tyr missense_variant 1.0
clpC1 4038630 p.Arg692Leu missense_variant 0.15
clpC1 4038761 c.1944C>A synonymous_variant 0.33
clpC1 4040135 c.570C>A synonymous_variant 0.29
clpC1 4040240 c.465C>T synonymous_variant 0.15
clpC1 4040636 c.69C>A synonymous_variant 0.29
panD 4044469 c.-188G>T upstream_gene_variant 0.2
embC 4239665 c.-198G>T upstream_gene_variant 0.17
embC 4239878 p.Ala6Ser missense_variant 0.17
embC 4240545 p.Pro228Gln missense_variant 0.25
embC 4240668 p.Ser269* stop_gained 0.25
embC 4242431 p.Gly857Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242927 p.Ser1022* stop_gained 0.29
embA 4243197 c.-36C>A upstream_gene_variant 0.18
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244222 c.990G>T synonymous_variant 0.22
embA 4244768 p.Glu512Asp missense_variant 0.17
embA 4244859 p.Gly543Trp missense_variant 0.25
embA 4244916 c.1684C>T synonymous_variant 0.25
embA 4245116 c.1886delA frameshift_variant 0.18
embA 4245573 p.Leu781Ile missense_variant 0.17
embA 4245855 p.Gly875Cys missense_variant 0.2
embA 4246477 p.Pro1082His missense_variant 0.18
embB 4246976 p.Ala155Ser missense_variant 0.15
embB 4247304 p.Gly264Val missense_variant 0.13
embB 4248930 p.Pro806His missense_variant 0.18
embB 4249006 c.2493G>T synonymous_variant 0.33
embB 4249213 c.2700C>A synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267785 p.Gly351Val missense_variant 0.15
aftB 4268355 p.Pro161Gln missense_variant 0.29
aftB 4268489 c.348C>A synonymous_variant 0.2
aftB 4268616 p.Gly74Val missense_variant 0.4
ubiA 4269942 c.-109C>A upstream_gene_variant 0.2
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338605 c.-84C>A upstream_gene_variant 0.18
whiB6 4338675 c.-154C>A upstream_gene_variant 0.2
whiB6 4338683 c.-162G>A upstream_gene_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408046 p.Ala53Thr missense_variant 0.22