TB-Profiler result

Run: SRR7131047
Summary

Run ID: SRR7131047

Sample name:

Date: 04-04-2023 18:43:13

Number of reads: 2815987

Percentage reads mapped: 100.0

Strain: lineage4.3.3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.87 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.73 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 1.0 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576516 p.Val390Ala missense_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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.24
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.24
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.29
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.27
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.35
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.51
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.7
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.7
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.65
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.63
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.63
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.63
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.52
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.56
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.54
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.41
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.44
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.7
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.72
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.72
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.72
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.74
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.72
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.68
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.36
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.11
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.55
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.55
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.63
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.63
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.4
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.12
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.19
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.28
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.79
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.87
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.87
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.87
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.79
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.69
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.21
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.61
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.12
rrs 1473201 n.1357C>T non_coding_transcript_exon_variant 0.15
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.12
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.24
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.5
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.38
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.43
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.43
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.18
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.18
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.18
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.3
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.57
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.59
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.48
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.52
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.62
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.64
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.5
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.4
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.29
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.27
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.29
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.29
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.31
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.27
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.69
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.73
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.68
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.64
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.63
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.66
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.66
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.66
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.48
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.69
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.87
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.9
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.88
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.86
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.86
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.81
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.69
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.45
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G 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
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
embA 4243392 p.Asn54Asp missense_variant 1.0
ubiA 4269731 p.Ala35Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0