TB-Profiler result

Run: ERR4814739
Summary

Run ID: ERR4814739

Sample name:

Date: 01-04-2023 13:27:50

Number of reads: 565629

Percentage reads mapped: 98.63

Strain: lineage2.2

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 0.99
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 761139 p.His445Ser missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326552 c.921delC frameshift_variant 0.15 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 7201 p.Glu654Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7455 p.His52Asn missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7637 c.336C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9326 c.2025G>T synonymous_variant 0.18
gyrA 9447 p.Val716Ile missense_variant 0.17
gyrA 9641 c.2340C>A synonymous_variant 0.2
fgd1 491628 p.Lys282Asn missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575511 p.Ser55* stop_gained 0.29
mshA 575767 c.420G>A synonymous_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576646 c.1299C>A synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620671 p.Trp261Arg missense_variant 0.33
rpoB 760667 p.Gln287His missense_variant 0.15
rpoB 761754 p.Asp650His missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765388 p.Phe673Leu missense_variant 0.25
rpoC 765752 p.Asp795Tyr missense_variant 0.13
rpoC 765755 p.Asp796Tyr missense_variant 0.14
rpoC 766363 c.2994G>T synonymous_variant 0.29
rpoC 766531 c.3162G>T synonymous_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 777313 p.Pro390Thr missense_variant 0.4
mmpL5 777548 c.933G>T synonymous_variant 0.33
mmpL5 777566 c.915C>A synonymous_variant 0.29
mmpL5 777701 c.780C>A synonymous_variant 0.29
mmpR5 778118 c.-872G>T upstream_gene_variant 0.29
mmpR5 779357 p.Arg123Met missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781640 p.Ser27Arg missense_variant 0.29
fbiC 1302788 c.-143C>A upstream_gene_variant 0.25
fbiC 1303743 c.813C>T synonymous_variant 0.15
fbiC 1304038 p.Pro370Thr missense_variant 0.22
fbiC 1305238 p.His770Asp missense_variant 0.15
Rv1258c 1406729 c.612G>T synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407321 p.Gly7Val missense_variant 0.33
Rv1258c 1407448 c.-108C>T upstream_gene_variant 0.29
Rv1258c 1407497 c.-157A>C upstream_gene_variant 0.33
embR 1417474 c.-127C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472166 n.321C>A non_coding_transcript_exon_variant 0.2
rrs 1472360 n.515G>C non_coding_transcript_exon_variant 0.12
rrs 1472505 n.660G>T non_coding_transcript_exon_variant 0.14
rrs 1472535 n.690C>G non_coding_transcript_exon_variant 0.14
rrl 1473609 n.-49G>T upstream_gene_variant 0.14
rrl 1474549 n.892G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>G non_coding_transcript_exon_variant 0.13
rrl 1474938 n.1281G>T non_coding_transcript_exon_variant 0.15
rrl 1476436 n.2779A>T non_coding_transcript_exon_variant 0.14
inhA 1674458 p.Asn86Ile missense_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834228 c.687C>A synonymous_variant 0.17
tlyA 1917885 c.-55G>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918239 c.300G>A synonymous_variant 0.33
tlyA 1918483 p.Lys182Glu missense_variant 0.22
tlyA 1918684 c.745C>A synonymous_variant 0.29
ndh 2101962 p.Pro361Ser missense_variant 0.15
katG 2153921 p.Val731Leu missense_variant 0.18
katG 2154639 c.1473C>A synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154788 p.Val442Phe missense_variant 0.15
katG 2155118 p.Phe332Leu missense_variant 0.11
PPE35 2167817 c.2796C>A synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168325 p.Asp763Gly missense_variant 0.33
PPE35 2168442 p.Trp724Leu missense_variant 0.14
PPE35 2168863 c.1750C>T synonymous_variant 0.14
PPE35 2169162 p.Ser484* stop_gained 0.29
PPE35 2169913 p.Asn234Asp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289904 c.-663G>C upstream_gene_variant 0.22
kasA 2518360 p.Tyr82* stop_gained 0.17
eis 2714510 c.823T>C synonymous_variant 0.11
eis 2714967 p.Glu122Asp missense_variant 0.25
eis 2715207 c.126C>G synonymous_variant 0.25
folC 2746902 p.Val233Phe missense_variant 0.4
folC 2747180 p.Ala140Val missense_variant 0.2
folC 2747373 p.Thr76Pro missense_variant 0.12
folC 2747459 p.Leu47Pro missense_variant 0.13
folC 2747561 p.Ser13* stop_gained 0.27
pepQ 2859765 c.654G>A synonymous_variant 0.18
pepQ 2859826 p.Ala198Asp missense_variant 0.15
pepQ 2859836 p.Ala195Pro missense_variant 0.2
ribD 2986678 c.-161C>A upstream_gene_variant 0.25
ribD 2987099 c.261C>T synonymous_variant 0.33
Rv2752c 3064848 p.Phe448Leu missense_variant 0.22
Rv2752c 3064875 c.1317C>A synonymous_variant 0.14
Rv2752c 3065148 c.1044C>A synonymous_variant 0.15
Rv2752c 3066261 c.-70G>T upstream_gene_variant 0.4
Rv2752c 3066287 c.-96G>T upstream_gene_variant 0.4
thyA 3073793 p.Tyr227His missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086811 c.-9G>T upstream_gene_variant 0.14
ald 3086824 p.Arg2Pro missense_variant 0.14
ald 3086886 p.Val23Phe missense_variant 0.17
ald 3087003 p.Asp62Tyr missense_variant 0.33
Rv3083 3448382 c.-122G>T upstream_gene_variant 0.18
Rv3083 3449552 p.Ile350Asn missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474538 p.Ile178Phe missense_variant 0.14
fprA 3474754 p.Lys250Glu missense_variant 0.2
fprA 3474954 p.Gln316His missense_variant 0.29
Rv3236c 3612405 p.Ala238Ser missense_variant 0.33
Rv3236c 3612701 p.Asp139Val missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612838 c.279G>T synonymous_variant 0.29
Rv3236c 3613111 p.Glu2Asp missense_variant 0.17
fbiB 3641076 c.-459C>A upstream_gene_variant 0.3
fbiA 3641308 p.Ala256Ser missense_variant 0.22
fbiB 3642843 p.Asp437Tyr missense_variant 0.29
alr 3840303 p.Glu373Gly missense_variant 0.33
alr 3840992 c.429C>T synonymous_variant 0.25
alr 3841371 p.Gly17Ala missense_variant 0.11
alr 3841407 p.Trp5Ser missense_variant 0.12
ddn 3987024 p.Val61Phe missense_variant 0.2
ddn 3987152 c.313_316delGAAG frameshift_variant 0.29
clpC1 4038449 c.2256C>T synonymous_variant 0.14
clpC1 4040348 c.357G>C synonymous_variant 0.4
clpC1 4040626 p.Tyr27His missense_variant 0.13
embC 4240626 p.Asp255Ala missense_variant 0.67
embC 4241944 c.2082C>A synonymous_variant 0.12
embA 4242310 c.-923C>T upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244666 c.1434G>C synonymous_variant 0.4
embB 4246403 c.-111G>T upstream_gene_variant 0.18
embB 4246882 c.369G>C synonymous_variant 0.22
embB 4247043 p.Pro177His missense_variant 0.25
embB 4248214 c.1704_1705delCG frameshift_variant 0.15
embB 4249051 c.2538C>T synonymous_variant 0.18
aftB 4267139 c.1698G>A synonymous_variant 0.22
aftB 4267409 c.1428C>T synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267743 p.Arg365Pro missense_variant 0.2
aftB 4268528 c.309C>A synonymous_variant 0.5
aftB 4268798 c.39C>A synonymous_variant 0.14
aftB 4269444 c.-608C>A upstream_gene_variant 0.17
ubiA 4269452 p.Met128Val missense_variant 0.18
ethA 4326123 p.Ser451Pro missense_variant 0.14
ethR 4326639 c.-910G>T upstream_gene_variant 0.33
ethA 4326648 p.Tyr276Asp missense_variant 0.29
ethA 4327467 p.Glu3* stop_gained 0.3
ethA 4328286 c.-813G>C upstream_gene_variant 0.13
ethA 4328294 c.-821C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407584 p.Arg207Ser missense_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407998 p.Gly69Ser missense_variant 0.22
gid 4408115 p.Gly30Cys missense_variant 0.2