TB-Profiler result

Run: SRR19303813
Summary

Run ID: SRR19303813

Sample name:

Date: 03-04-2023 21:07:40

Number of reads: 1991908

Percentage reads mapped: 28.93

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155693 p.Ser140Asn missense_variant 0.15 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 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.14
rpoB 760975 p.Met390Thr missense_variant 1.0
rpoC 764611 c.1242G>C synonymous_variant 0.27
rpoC 764632 c.1263T>C synonymous_variant 0.23
rpoC 764644 c.1275G>C synonymous_variant 0.24
rpoC 764650 c.1281G>T synonymous_variant 0.25
rpoC 764656 c.1287C>G synonymous_variant 0.25
rpoC 764662 c.1293G>C synonymous_variant 0.24
rpoC 764668 c.1299C>T synonymous_variant 0.24
rpoC 764671 c.1302G>C synonymous_variant 0.24
rpoC 764672 p.Gln435Glu missense_variant 0.24
rpoC 764677 c.1308C>G synonymous_variant 0.24
rpoC 764686 c.1317C>T synonymous_variant 0.23
rpoC 764695 c.1326T>C synonymous_variant 0.25
rpoC 764701 c.1332C>G synonymous_variant 0.25
rpoC 764705 p.Leu446Lys missense_variant 0.23
rpoC 764716 c.1347G>C synonymous_variant 0.2
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 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.13
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.13
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.14
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.15
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrl 1473412 n.-245delG upstream_gene_variant 0.17
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475090 n.1433A>C non_coding_transcript_exon_variant 1.0
rrl 1476219 n.2562T>C non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.19
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.19
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.2
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.2
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.19
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.2
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.2
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.19
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.28
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.31
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.31
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.59
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.62
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.62
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.56
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.58
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.61
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.56
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.56
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.49
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.5
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.47
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.44
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155655 p.Lys153Gln missense_variant 0.12
katG 2155661 p.Val151Ile missense_variant 0.12
katG 2155674 c.438G>T synonymous_variant 0.15
katG 2155680 p.Ala144Gly missense_variant 0.15
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.15
katG 2155704 c.408C>G synonymous_variant 0.16
katG 2155710 c.400_402delAGCinsTCG synonymous_variant 0.15
katG 2155716 c.396T>C synonymous_variant 0.15
katG 2155728 c.384G>C synonymous_variant 0.14
katG 2155735 p.Met126Gln missense_variant 0.13
katG 2155737 c.375C>A synonymous_variant 0.13
katG 2155741 p.Gly124Thr missense_variant 0.13
katG 2155743 c.369G>C synonymous_variant 0.13
katG 2155765 p.His116Pro missense_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086767 c.-53A>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fbiD 3339746 p.Ala210Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244990 c.1758G>C synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.38
aftB 4267715 c.1122G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0