TB-Profiler result

Run: ERR4832067
Summary

Run ID: ERR4832067

Sample name:

Date: 01-04-2023 21:18:03

Number of reads: 572955

Percentage reads mapped: 78.78

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155999 p.Trp38* stop_gained 0.18 isoniazid
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 5710 c.471C>G synonymous_variant 0.15
gyrA 6460 c.-842G>T upstream_gene_variant 0.33
gyrA 6916 c.-386G>C upstream_gene_variant 0.12
gyrB 6922 c.1688delT frameshift_variant 0.13
gyrB 6979 p.Phe580Leu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8645 c.1344C>G synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491284 p.Gly168Arg missense_variant 0.2
fgd1 491289 c.507C>A synonymous_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491746 p.Glu322* stop_gained 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762487 p.Pro894Gln missense_variant 0.12
rpoB 762522 p.Pro906Thr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765725 p.Gly786Ser missense_variant 0.14
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 776418 p.Ser688* stop_gained 0.29
mmpL5 776695 p.Val596Phe missense_variant 0.14
mmpL5 778918 c.-438G>T upstream_gene_variant 0.33
mmpR5 779192 p.Ser68Ile missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781444 c.-116C>A upstream_gene_variant 0.13
rpsL 781453 c.-107C>G upstream_gene_variant 0.13
rpsL 781465 c.-95G>T upstream_gene_variant 0.13
rplC 800921 p.Arg38His missense_variant 0.18
rplC 800967 c.159C>A synonymous_variant 0.12
fbiC 1304672 p.Val581Ala missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416232 c.1116T>C synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471870 n.25G>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472861 n.1016G>T non_coding_transcript_exon_variant 0.2
rrs 1472885 n.1040T>C non_coding_transcript_exon_variant 0.17
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrl 1474097 n.440C>A non_coding_transcript_exon_variant 0.67
rrl 1474904 n.1247G>T non_coding_transcript_exon_variant 0.33
rrl 1475721 n.2064C>A non_coding_transcript_exon_variant 0.5
fabG1 1673944 p.Arg169Cys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834352 c.811C>A synonymous_variant 0.12
rpsA 1834535 p.Glu332* stop_gained 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102449 p.Lys198Asn missense_variant 0.17
ndh 2102772 p.His91Asn missense_variant 0.18
katG 2154389 p.Ser575Pro missense_variant 0.12
katG 2154426 p.Asn562Lys missense_variant 0.13
katG 2154703 p.Ser470Leu missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154780 c.1332G>A synonymous_variant 0.14
PPE35 2167743 p.Gly957Val missense_variant 0.12
PPE35 2167886 p.Phe909Leu missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168579 c.2034C>A synonymous_variant 0.12
PPE35 2168604 p.Pro670His missense_variant 0.13
PPE35 2169032 p.Phe527Leu missense_variant 0.22
PPE35 2169560 c.1053G>T synonymous_variant 0.4
PPE35 2170581 p.Asn11Ser missense_variant 0.1
Rv1979c 2222680 p.Ala162Asp missense_variant 0.25
Rv1979c 2222927 p.Ala80Ser missense_variant 0.12
Rv1979c 2222947 p.Arg73Lys missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223330 c.-166C>T upstream_gene_variant 0.33
pncA 2289294 c.-53G>C upstream_gene_variant 0.12
pncA 2290204 c.-963G>A upstream_gene_variant 0.22
pncA 2290210 c.-969G>A upstream_gene_variant 0.2
kasA 2518195 c.81G>A synonymous_variant 0.5
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726670 p.Glu160* stop_gained 0.13
ahpC 2726735 c.543C>A synonymous_variant 0.12
ahpC 2726773 p.Ser194Leu missense_variant 0.13
Rv2752c 3064596 c.1596G>T synonymous_variant 0.12
Rv2752c 3064908 p.Ser428Arg missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087053 p.Ile78Met missense_variant 0.2
Rv3083 3448312 c.-192T>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568408 p.Val91Ala missense_variant 0.11
whiB7 3568648 p.Pro11Arg missense_variant 0.2
whiB7 3568772 c.-93C>A upstream_gene_variant 0.67
Rv3236c 3612391 c.726G>T synonymous_variant 0.15
Rv3236c 3612425 p.Ala231Glu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878268 c.240C>A synonymous_variant 0.33
ddn 3987125 c.282C>A synonymous_variant 0.18
clpC1 4038643 p.Asn688Asp missense_variant 0.33
clpC1 4039752 p.Gln318Arg missense_variant 0.11
panD 4043995 p.Ala96Asp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245175 p.Ser648* stop_gained 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249550 p.Arg1013Ser missense_variant 0.13
embB 4249739 p.Ala1076Ser missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326290 p.Ala395Asp missense_variant 0.12
ethR 4327369 c.-180C>T upstream_gene_variant 0.12
ethA 4327638 c.-165G>T upstream_gene_variant 0.14
whiB6 4338286 p.Val79Asp missense_variant 0.12
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