TB-Profiler result

Run: SRR11972159
Summary

Run ID: SRR11972159

Sample name:

Date: 03-04-2023 05:30:23

Number of reads: 533754

Percentage reads mapped: 98.41

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 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288936 c.305delC frameshift_variant 1.0 pyrazinamide, pyrazinamide
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
gyrB 6852 p.Gln538Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575427 p.Ser27Leu missense_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620402 p.Trp171* stop_gained 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760249 c.446dupG frameshift_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776087 c.2394C>G synonymous_variant 0.25
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776342 c.2139G>A synonymous_variant 0.33
mmpR5 779428 p.Glu147* stop_gained 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781926 p.Lys123Glu missense_variant 0.14
fbiC 1303383 c.453G>A synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417514 c.-167C>T upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>G non_coding_transcript_exon_variant 0.15
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.28
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.24
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.15
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.21
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.2
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.2
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.2
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.18
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.31
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.4
rrs 1472601 n.756G>T non_coding_transcript_exon_variant 0.12
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472819 n.974T>A non_coding_transcript_exon_variant 0.18
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.12
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.14
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.13
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.25
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834691 p.Tyr384Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.13
ndh 2103090 c.-48G>T upstream_gene_variant 0.12
ndh 2103158 c.-116C>A upstream_gene_variant 0.14
katG 2154149 p.Asn655Asp missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.29
PPE35 2167760 c.2853G>A synonymous_variant 0.29
PPE35 2167763 p.Ile950Val missense_variant 0.29
PPE35 2167784 c.2829C>T synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168213 c.2400G>A synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169293 c.1320T>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170147 p.Ser156Ala missense_variant 0.19
PPE35 2170157 p.Ala152Ser missense_variant 0.13
PPE35 2170164 p.Ala150Val missense_variant 0.12
PPE35 2170220 c.393C>G synonymous_variant 0.12
PPE35 2170223 c.390T>C synonymous_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.15
PPE35 2170247 p.Ile122Met missense_variant 0.12
PPE35 2170400 c.213G>C synonymous_variant 0.18
PPE35 2170540 c.73C>T synonymous_variant 0.18
Rv1979c 2222032 c.1132delG frameshift_variant 0.13
Rv1979c 2222723 c.442C>T synonymous_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289262 c.-21G>T upstream_gene_variant 0.2
pncA 2289742 c.-501G>A upstream_gene_variant 0.15
eis 2715222 c.111G>A synonymous_variant 0.15
eis 2715425 c.-93G>T upstream_gene_variant 0.12
folC 2746241 p.Asp453Gly missense_variant 0.4
Rv2752c 3064969 p.Lys408Arg missense_variant 0.22
thyA 3074207 p.Glu89Lys missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339058 c.-60G>A upstream_gene_variant 0.15
fbiD 3339339 c.222G>T synonymous_variant 0.25
fbiD 3339738 c.621C>A synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642615 p.Pro361Thr missense_variant 0.33
alr 3840813 p.Pro203His missense_variant 0.14
alr 3841442 c.-22G>A upstream_gene_variant 0.14
rpoA 3877806 c.702C>T synonymous_variant 0.17
rpoA 3877969 p.Ala180Val missense_variant 1.0
ddn 3986822 c.-22C>A upstream_gene_variant 0.14
clpC1 4039177 p.Met510Leu missense_variant 0.15
clpC1 4039645 p.His354Asp missense_variant 0.12
panD 4044393 c.-112G>A upstream_gene_variant 0.33
embC 4240456 c.594C>T synonymous_variant 0.14
embC 4240789 c.927T>C synonymous_variant 0.18
embC 4240793 p.Ala311Ser missense_variant 0.22
embC 4240801 c.939C>T synonymous_variant 0.17
embC 4240803 p.Tyr314Phe missense_variant 0.17
embC 4240853 c.991C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244816 c.1584G>A synonymous_variant 1.0
embB 4246481 c.-33C>T upstream_gene_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4247854 c.1341C>A synonymous_variant 0.2
aftB 4267149 p.Glu563Val missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.9
aftB 4268640 p.Leu66Gln missense_variant 0.33
ethR 4328011 p.Ala155Pro missense_variant 0.17
ethA 4328275 c.-802G>A upstream_gene_variant 0.22
whiB6 4338394 p.Thr43Met missense_variant 1.0
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