TB-Profiler result

Run: SRR1002700
Summary

Run ID: SRR1002700

Sample name:

Date: 02-04-2023 14:20:03

Number of reads: 354543

Percentage reads mapped: 98.44

Strain: lineage2.2.1

Drug-resistance: HR-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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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
gyrA 6922 c.-380G>T upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9290 c.1989G>T synonymous_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9333 p.Gly678Trp missense_variant 0.29
fgd1 491355 c.573C>A synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575416 c.69T>C synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620620 p.Val244Met missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761943 c.2137C>T synonymous_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763301 c.-69C>G upstream_gene_variant 0.2
rpoC 765244 c.1875T>A synonymous_variant 0.29
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775712 c.2769G>A synonymous_variant 0.2
mmpL5 775826 c.2655G>A synonymous_variant 0.2
mmpL5 775871 c.2610C>T synonymous_variant 0.22
mmpL5 775874 c.2607C>A synonymous_variant 0.22
mmpL5 776003 c.2478C>T synonymous_variant 0.18
mmpL5 776008 p.His825Asp missense_variant 0.17
mmpL5 776009 c.2472A>G synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776670 p.Phe604Ser missense_variant 0.11
mmpL5 777563 c.918C>T synonymous_variant 0.22
mmpR5 779062 p.Gly25Cys missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.33
fbiC 1305038 p.Arg703Leu missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473221 n.1376C>A non_coding_transcript_exon_variant 0.14
rrl 1473722 n.65G>C non_coding_transcript_exon_variant 0.15
rrl 1473727 n.70G>A non_coding_transcript_exon_variant 0.15
rrl 1475024 n.1367G>T non_coding_transcript_exon_variant 0.15
rrl 1475187 n.1530C>A non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
fabG1 1673899 p.Ala154Ser missense_variant 0.29
inhA 1674376 p.Pro59Ala missense_variant 0.25
inhA 1674567 c.366C>A synonymous_variant 0.2
rpsA 1833388 c.-154C>A upstream_gene_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834610 p.Arg357Trp missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917981 c.42G>C synonymous_variant 0.25
ndh 2103120 c.-78C>A upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155578 c.534C>T synonymous_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167931 c.2682C>T synonymous_variant 0.12
PPE35 2167936 p.Thr893Ala missense_variant 0.11
PPE35 2167937 c.2676A>C synonymous_variant 0.11
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2169779 c.834A>C synonymous_variant 0.15
PPE35 2169831 p.Asn261Ile missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170187 c.426G>A synonymous_variant 0.13
PPE35 2170193 p.Tyr140* stop_gained 0.12
PPE35 2170544 c.69G>A synonymous_variant 0.13
PPE35 2170547 c.66A>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289367 c.-126C>A upstream_gene_variant 0.14
kasA 2518864 c.750G>C synonymous_variant 0.15
kasA 2518879 c.765A>G synonymous_variant 0.13
kasA 2518882 c.768C>A synonymous_variant 0.13
kasA 2519128 c.1014G>C synonymous_variant 0.2
kasA 2519131 c.1017G>C synonymous_variant 0.22
eis 2714278 p.Asp352Gly missense_variant 0.17
eis 2715068 p.Pro89Thr missense_variant 0.14
eis 2715540 c.-208C>T upstream_gene_variant 0.4
ahpC 2726335 p.Arg48Leu missense_variant 0.14
folC 2746318 c.1281C>A synonymous_variant 0.15
ribD 2986928 p.Gln30His missense_variant 0.33
ribD 2987173 p.Ser112Asn missense_variant 0.33
Rv2752c 3064949 p.Val415Ile missense_variant 0.14
Rv2752c 3065480 p.Phe238Leu missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339442 p.Asn109Asp missense_variant 0.14
fbiD 3339547 p.Leu144Phe missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568577 p.Gly35Cys missense_variant 0.17
Rv3236c 3612149 p.Gln323Arg missense_variant 0.12
Rv3236c 3612282 p.Gly279Ser missense_variant 0.14
Rv3236c 3612289 c.828G>T synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641609 c.75C>A synonymous_variant 0.15
fbiB 3641647 p.Pro38Gln missense_variant 0.17
fbiB 3642415 p.Pro294Leu missense_variant 0.17
alr 3840691 p.Pro244Thr missense_variant 0.2
alr 3841018 c.403C>T synonymous_variant 0.22
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
rpoA 3877769 p.Phe247Leu missense_variant 0.4
ddn 3987030 p.Pro63Thr missense_variant 0.14
clpC1 4039003 p.Asn568Asp missense_variant 0.16
clpC1 4039498 p.Ile403Val missense_variant 0.18
clpC1 4039682 c.1023C>T synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.18
embC 4239834 c.-29G>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244208 p.Leu326Met missense_variant 0.5
embA 4244219 c.987C>A synonymous_variant 0.5
embA 4245081 p.Ala617Thr missense_variant 0.4
embA 4246449 p.Val1073Phe missense_variant 0.13
embB 4247375 p.Leu288Met missense_variant 0.15
embB 4249022 p.Leu837Ile missense_variant 0.33
aftB 4267103 c.1734G>T synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267708 p.Gly377Trp missense_variant 0.22
aftB 4268283 p.Val185Ala missense_variant 0.15
ubiA 4269566 p.Arg90Trp missense_variant 0.33
ethA 4327235 p.Pro80His missense_variant 0.2
ethR 4327432 c.-117G>A upstream_gene_variant 0.22
ethR 4327961 p.Trp138Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338685 c.-164C>A upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0