TB-Profiler result

Run: SRR3086370
Summary

Run ID: SRR3086370

Sample name:

Date: 04-04-2023 05:01:07

Number of reads: 841328

Percentage reads mapped: 81.21

Strain: lineage4

Drug-resistance: Pre-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
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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289156 c.85dupC frameshift_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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
mshA 575729 p.Gln128Lys missense_variant 0.33
rpoB 760510 p.Leu235Pro missense_variant 0.33
rpoB 762523 p.Pro906Gln missense_variant 0.14
rpoC 765618 p.Glu750Gly missense_variant 1.0
mmpL5 775732 p.Asp917Asn missense_variant 0.33
mmpL5 775778 c.2703C>A synonymous_variant 0.5
mmpL5 776580 p.Leu634Gln missense_variant 0.15
mmpL5 777022 p.Pro487Thr missense_variant 0.29
mmpL5 778075 p.Ala136Ser missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416521 p.Val276Glu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472500 n.655G>A non_coding_transcript_exon_variant 0.14
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.13
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.38
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.21
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.13
rrs 1472921 n.1076T>A non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.15
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.33
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.33
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.22
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.4
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.29
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.43
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.43
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.33
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.3
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
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 0.22
rpsA 1834182 p.Gly214Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.15
PPE35 2167826 c.2787C>G synonymous_variant 0.5
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169675 p.Asn313Ser missense_variant 0.15
Rv1979c 2222771 p.Gln132Glu missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746347 p.Ala418Pro missense_variant 0.25
pepQ 2859878 p.Leu181Phe missense_variant 0.5
ribD 2986978 p.Ser47Ile missense_variant 0.17
Rv2752c 3064515 c.1677A>C stop_lost&splice_region_variant 1.0
Rv2752c 3064806 c.1386G>A synonymous_variant 0.22
thyX 3067698 p.Thr83Asn missense_variant 1.0
fbiA 3640413 c.-130T>A upstream_gene_variant 0.18
fbiA 3640642 p.His34Asn missense_variant 0.22
clpC1 4039508 c.1197G>T synonymous_variant 0.13
embC 4241211 p.Leu450Gln missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4246916 p.Val135Met missense_variant 0.29
embB 4248694 c.2181G>A synonymous_variant 1.0
ethA 4327052 p.Tyr141Cys missense_variant 1.0
ethR 4327974 p.Met142Ile missense_variant 1.0
ethR 4327975 p.Gln143Lys missense_variant 1.0
whiB6 4338269 c.252delA frameshift_variant 1.0
whiB6 4338466 p.Val19Glu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0