TB-Profiler result

Run: SRR9971101

Summary

Run ID: SRR9971101

Sample name:

Date: 04-04-2023 23:11:23

Number of reads: 5227073

Percentage reads mapped: 48.26

Strain: lineage4.1.2.1

Drug-resistance: XDR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.19 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
pncA 2289140 p.Tyr34* stop_gained 0.14 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu missense_variant 1.0 streptomycin
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576754 c.1407C>A synonymous_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762639 p.Gly945Trp missense_variant 0.15
rpoC 764590 p.Lys407Asn missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777278 c.1203G>T synonymous_variant 0.18
mmpL5 777293 c.1188T>C synonymous_variant 0.17
mmpL5 777301 p.Leu394Met missense_variant 0.17
mmpL5 777311 c.1170C>A synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303121 p.Arg64Leu missense_variant 0.18
fbiC 1305204 c.2274C>A synonymous_variant 0.15
fbiC 1305291 p.Ser787Arg missense_variant 0.13
Rv1258c 1406282 c.1059G>T synonymous_variant 0.12
Rv1258c 1406292 p.Gly350Val missense_variant 0.14
Rv1258c 1406813 c.528T>C synonymous_variant 1.0
Rv1258c 1406998 p.Ala115Thr missense_variant 0.13
Rv1258c 1407072 p.Pro90His missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.11
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.16
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.16
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.17
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.16
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.16
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.15
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.16
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.13
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.14
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.15
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.15
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.15
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.15
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.11
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.24
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.22
PPE35 2170401 p.Pro71Gln missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714769 c.564C>G synonymous_variant 0.11
Rv2752c 3065786 p.His136Asn missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 0.93
rpoA 3878551 c.-44C>A upstream_gene_variant 0.15
embC 4239969 c.110delG frameshift_variant 0.1
embC 4240411 c.549G>C synonymous_variant 0.24
embC 4241126 p.Leu422Met missense_variant 0.13
embA 4242334 c.-899G>T upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243078 c.-155C>G upstream_gene_variant 0.12
embA 4243733 c.501G>A synonymous_variant 0.14
embA 4245763 p.Gly844Val missense_variant 0.17
embB 4246565 p.Gly18Trp missense_variant 0.17
embB 4247738 p.Ala409Pro missense_variant 1.0
embB 4249567 c.3054C>T synonymous_variant 0.13
ubiA 4268948 p.Gly296Trp missense_variant 0.2
ethA 4326842 p.Tyr211Ser missense_variant 0.97
whiB6 4338300 c.222G>T synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0