TB-Profiler result

Run: SRR6339665

Summary

Run ID: SRR6339665

Sample name:

Date: 04-04-2023 13:29:55

Number of reads: 840620

Percentage reads mapped: 90.28

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4248003 p.Gln497Arg 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 9304 p.Gly668Asp missense_variant 1.0
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 760900 p.Asp365Ala missense_variant 0.29
rpoC 762572 c.-798C>A upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763088 c.-282C>T upstream_gene_variant 0.12
rpoC 764628 p.Lys420Arg missense_variant 0.12
rpoC 767223 p.Ile1285Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776175 p.Ser769Tyr missense_variant 0.15
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778661 p.Asp82Ala missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.6
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.83
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.7
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.8
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.78
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.8
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.8
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.8
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.8
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.8
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.8
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.8
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.8
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.8
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.75
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.8
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.82
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.86
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.88
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.88
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.85
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476415 n.2758C>T non_coding_transcript_exon_variant 0.14
rrl 1476416 n.2759C>T non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.83
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.83
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.56
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.33
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.29
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.25
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.25
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.25
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.25
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.25
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.22
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.18
inhA 1674326 p.Asp42Ala missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834969 p.Lys476Asn missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102937 p.Ala36Pro missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154789 c.1323G>A synonymous_variant 0.13
katG 2155541 p.Trp191Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168542 p.Thr691Ser missense_variant 0.33
PPE35 2168773 p.Leu614Ile missense_variant 0.17
Rv1979c 2222640 c.525G>C synonymous_variant 0.13
Rv1979c 2223215 c.-51T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746218 p.Phe461Ile missense_variant 0.17
folC 2746813 p.Glu262Asp missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474233 p.Phe76Ser missense_variant 0.1
fprA 3474471 c.465T>C synonymous_variant 1.0
whiB7 3568566 c.114A>C synonymous_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640439 c.-104C>T upstream_gene_variant 0.11
fbiB 3641953 p.Leu140Arg missense_variant 0.29
rpoA 3878490 c.18C>A synonymous_variant 0.4
clpC1 4039034 c.1671C>T synonymous_variant 0.11
embC 4240950 p.Val363Gly missense_variant 0.15
embC 4242414 p.Leu851Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245686 c.-828G>A upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326992 p.Ile161Ser missense_variant 0.2
ethA 4327470 p.Thr2Pro missense_variant 0.5
ethA 4328304 c.-831A>C upstream_gene_variant 0.17
whiB6 4338552 c.-31A>G upstream_gene_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