TB-Profiler result

Run: SRR1169150
Summary

Run ID: SRR1169150

Sample name:

Date: 03-04-2023 02:47:43

Number of reads: 1377559

Percentage reads mapped: 87.52

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 781822 p.Lys88Arg missense_variant 0.94 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.93 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_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
gyrB 6144 p.His302Arg missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 766485 p.Val1039Ala missense_variant 1.0
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 1472697 n.852T>G non_coding_transcript_exon_variant 0.13
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.12
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.32
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.19
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.12
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 1476293 n.2636C>T non_coding_transcript_exon_variant 0.15
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.16
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.28
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.3
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.35
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rrl 1476565 n.2908G>A non_coding_transcript_exon_variant 0.13
rrl 1476566 n.2909A>G non_coding_transcript_exon_variant 0.14
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.14
rrl 1476577 n.2920T>A non_coding_transcript_exon_variant 0.12
rrl 1476578 n.2921C>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rrl 1476592 n.2935G>A non_coding_transcript_exon_variant 0.13
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.13
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.12
rrl 1476605 n.2948C>T non_coding_transcript_exon_variant 0.12
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.12
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.12
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
rrl 1476637 n.2980C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2156117 c.-6A>G upstream_gene_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086635 c.-185_-184insA upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3641348 p.Ala269Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4243844 p.Lys204Asn missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0