TB-Profiler result

Run: SRR847801
Summary

Run ID: SRR847801

Sample name:

Date: 04-04-2023 21:26:16

Number of reads: 8223627

Percentage reads mapped: 66.77

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.99 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.46 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.94 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.99 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 0.99 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.99 ethionamide
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 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 763123 p.Ile1106Thr missense_variant 0.99
rpoC 764995 c.1626C>G synonymous_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 1472545 n.700A>T non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.37
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.38
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.37
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.37
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.35
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.48
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.48
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.48
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.46
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.39
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.2
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.2
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.21
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.22
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.19
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.99
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.34
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.36
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.51
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.58
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.65
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.64
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.64
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.51
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.24
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.24
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.23
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.22
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.22
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.99
Rv2752c 3065824 p.Pro123Leu missense_variant 0.98
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087715 c.897dupG frameshift_variant 0.24
ald 3087895 c.1081dupG frameshift_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269271 p.Val188Ala missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407922 p.Leu94Gln missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0