TB-Profiler result

Run: ERR2984782
Summary

Run ID: ERR2984782

Sample name:

Date: 01-04-2023 00:06:22

Number of reads: 2113637

Percentage reads mapped: 92.08

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 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 7570 p.Ala90Val missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.14 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576160 c.813C>T synonymous_variant 1.0
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
rplC 800990 p.Lys61Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.15
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.23
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.1
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.14
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.17
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.15
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.16
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.13
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.11
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.11
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.12
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.15
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.18
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.15
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.16
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.16
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.2
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.11
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.1
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.1
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.17
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.23
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.23
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.23
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.19
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.19
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.19
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.21
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.22
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.2
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.21
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.1
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.1
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155321 p.Ala264Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289889 c.-661_-649dupTGACCGCCGCCGC upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877586 p.Leu308Phe missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0