TB-Profiler result

Run: ERR5866451
Summary

Run ID: ERR5866451

Sample name:

Date: 02-04-2023 00:41:36

Number of reads: 633216

Percentage reads mapped: 88.62

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 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.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289103 p.Thr47Ala missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
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 8495 c.1194C>A synonymous_variant 0.17
gyrA 8871 p.Gly524* stop_gained 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9683 c.2382G>T synonymous_variant 0.13
fgd1 491019 p.Phe79Leu missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761646 p.Arg614Ser missense_variant 0.17
rpoB 761895 p.Ala697Pro missense_variant 0.11
rpoC 762704 c.-666G>A upstream_gene_variant 0.38
rpoC 762818 c.-552C>A upstream_gene_variant 0.17
rpoB 762885 p.Leu1027Met missense_variant 0.2
rpoB 762987 p.Arg1061Trp missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776012 p.Trp823Cys missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776170 p.Gly771Cys missense_variant 0.17
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776205 p.Gly759Val missense_variant 0.18
mmpL5 776324 c.2157C>A synonymous_variant 0.22
mmpL5 777186 p.Ala432Glu missense_variant 0.14
mmpL5 777473 c.1008T>C synonymous_variant 0.1
mmpL5 777647 c.834C>A synonymous_variant 0.17
mmpL5 777836 c.645C>A synonymous_variant 0.15
mmpL5 778306 c.174delG frameshift_variant 0.22
mmpR5 779044 p.Phe19Leu missense_variant 0.14
mmpR5 779387 p.Ser133Ile missense_variant 0.15
mmpR5 779401 p.Glu138* stop_gained 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781854 p.Arg99Gly missense_variant 0.12
rplC 800673 c.-136G>T upstream_gene_variant 0.18
fbiC 1303977 c.1047C>A synonymous_variant 0.22
fbiC 1304316 c.1386G>T synonymous_variant 0.13
fbiC 1304802 c.1872G>T synonymous_variant 0.22
fbiC 1304820 c.1890G>T synonymous_variant 0.2
fbiC 1304871 c.1941G>T synonymous_variant 0.2
fbiC 1305054 p.Met708Ile missense_variant 0.2
fbiC 1305236 p.Val769Ala missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461162 p.Ala40Ser missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473515 n.-143G>T upstream_gene_variant 0.18
rrl 1474387 n.730C>A non_coding_transcript_exon_variant 0.15
rrl 1474667 n.1010G>T non_coding_transcript_exon_variant 0.15
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.2
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.2
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.25
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.25
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.25
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.33
rrl 1475150 n.1493C>A non_coding_transcript_exon_variant 0.33
rrl 1475335 n.1678G>T non_coding_transcript_exon_variant 0.13
rrl 1475647 n.1990G>T non_coding_transcript_exon_variant 0.14
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.17
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.17
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.17
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.17
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.17
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.18
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.18
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.18
rrl 1476060 n.2403T>G non_coding_transcript_exon_variant 0.25
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>A non_coding_transcript_exon_variant 0.22
rrl 1476394 n.2737C>T non_coding_transcript_exon_variant 0.15
inhA 1674957 c.756G>T synonymous_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918053 c.114G>A synonymous_variant 0.13
tlyA 1918298 p.Trp120Ser missense_variant 0.14
tlyA 1918561 p.Val208Leu missense_variant 0.12
ndh 2101755 p.Thr430Ser missense_variant 0.22
ndh 2102610 c.432G>A synonymous_variant 0.14
ndh 2102738 p.Glu102Gly missense_variant 0.12
ndh 2103112 c.-70G>T upstream_gene_variant 0.17
katG 2154309 c.1803C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155063 p.Ala350Asp missense_variant 0.22
katG 2155106 p.Leu336Met missense_variant 0.17
katG 2155197 c.915C>T synonymous_variant 0.14
katG 2156395 c.-284G>T upstream_gene_variant 0.18
katG 2156416 c.-305G>T upstream_gene_variant 0.15
PPE35 2167702 p.Ala971Ser missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168281 p.Pro778Thr missense_variant 0.15
PPE35 2168473 c.2139dupC frameshift_variant 0.22
PPE35 2169701 c.911delA frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518175 p.Ala21Ser missense_variant 0.17
kasA 2518573 c.459G>T synonymous_variant 0.14
eis 2714527 p.Thr269Asn missense_variant 0.13
eis 2714865 c.468C>A synonymous_variant 0.18
ahpC 2726239 p.Thr16Asn missense_variant 0.14
folC 2746581 p.Glu340* stop_gained 0.13
folC 2746687 c.912C>T synonymous_variant 0.14
folC 2746928 p.Pro224Leu missense_variant 0.25
folC 2747283 p.Glu106* stop_gained 0.15
ribD 2986711 c.-128G>A upstream_gene_variant 0.13
ribD 2987443 p.Phe202Ser missense_variant 0.18
ribD 2987574 p.Asp246Tyr missense_variant 0.2
Rv2752c 3065065 p.Ala376Val missense_variant 0.15
Rv2752c 3065706 c.486G>T synonymous_variant 0.14
Rv2752c 3065749 p.His148Pro missense_variant 1.0
thyX 3067208 p.Leu246Phe missense_variant 0.18
thyX 3067630 p.Gln106Lys missense_variant 0.2
thyX 3067745 c.201C>A synonymous_variant 0.33
thyX 3067754 c.192C>A synonymous_variant 0.33
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568630 p.Val17Ala missense_variant 0.12
Rv3236c 3612652 c.465G>T synonymous_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640672 p.Val44Ile missense_variant 0.15
fbiA 3641225 p.Gly228Glu missense_variant 0.14
fbiA 3641382 p.Cys280* stop_gained 0.15
fbiA 3641496 p.Glu318Asp missense_variant 0.17
rpoA 3877496 p.Glu338* stop_gained 0.17
clpC1 4038656 p.Lys683Asn missense_variant 0.14
clpC1 4039046 c.1659C>A synonymous_variant 0.14
clpC1 4039922 c.783C>T synonymous_variant 0.17
panD 4044446 c.-165C>A upstream_gene_variant 0.2
embC 4239834 c.-29G>T upstream_gene_variant 0.14
embC 4241296 c.1434C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242718 c.-515G>T upstream_gene_variant 0.18
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243352 c.120C>A synonymous_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244045 c.813G>T synonymous_variant 0.17
embA 4245128 c.1896G>T synonymous_variant 0.15
embB 4246049 c.-465G>A upstream_gene_variant 0.17
embB 4246548 p.Pro12Leu missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268471 c.366G>T synonymous_variant 0.17
ubiA 4269725 p.Leu37Met missense_variant 0.12
ubiA 4270005 c.-172C>A upstream_gene_variant 0.25
ethA 4326751 p.Lys241Asn missense_variant 0.15
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338665 c.-144C>T upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0