TB-Profiler result

Run: SRR10315728
Summary

Run ID: SRR10315728

Sample name:

Date: 02-04-2023 17:17:02

Number of reads: 5314861

Percentage reads mapped: 92.52

Strain: lineage4.8;lineage4.4.1.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.36
lineage4.4 Euro-American S;T None 0.65
lineage4.4.1 Euro-American (S-type) S;T None 0.64
lineage4.4.1.1 Euro-American S;Orphans None 0.62
lineage4.4.1.1.1 Euro-American S;Orphans None 0.61
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 0.45 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.36 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.12 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.38 isoniazid
embB 4247469 p.Tyr319Cys missense_variant 0.43 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 0.58
gyrA 9304 p.Gly668Asp missense_variant 0.67
rpoB 761002 p.Thr399Ile missense_variant 0.38
rpoC 766500 p.Ala1044Val missense_variant 0.45
rpoC 766872 p.Ile1168Asn missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.12
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.17
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.17
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.14
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.13
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
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 0.23
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.15
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.42
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.14
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.13
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.13
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.13
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.14
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.15
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.17
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.24
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.26
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.27
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.68
PPE35 2169840 p.Gly258Asp missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986778 c.-61G>A upstream_gene_variant 0.55
ald 3086788 c.-32T>C upstream_gene_variant 0.56
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.57
Rv3236c 3612665 p.Val151Ala missense_variant 0.61
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267149 p.Glu563Gly missense_variant 0.43
aftB 4267155 p.Gln561Arg missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0