TB-Profiler result

Run: SRR7131098
Summary

Run ID: SRR7131098

Sample name:

Date: 04-04-2023 18:45:07

Number of reads: 2518455

Percentage reads mapped: 100.0

Strain: lineage4.3.3

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
lineage4.3 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 1473246 n.1401A>G non_coding_transcript_exon_variant 0.95 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 576108 p.Ala254Gly missense_variant 0.15
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 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.11
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.2
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.1
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.16
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.16
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.16
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.11
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.12
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.43
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.3
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.25
rrl 1474280 n.623C>T non_coding_transcript_exon_variant 0.23
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.23
rrl 1474284 n.631_633delCCT non_coding_transcript_exon_variant 0.21
rrl 1474293 n.637_651delCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 0.18
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.15
rrl 1474317 n.660G>A non_coding_transcript_exon_variant 0.15
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.15
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.14
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.14
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.15
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474383 n.726G>T non_coding_transcript_exon_variant 0.12
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.12
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.14
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.14
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.17
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.17
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.17
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.14
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.11
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.3
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.17
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.26
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.19
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.11
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.19
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.11
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.1
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.23
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.17
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.17
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.12
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.19
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.23
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.32
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.35
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.35
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.35
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.29
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.21
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.19
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.19
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.19
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.13
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.13
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.14
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.14
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.14
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.13
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.1
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.1
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.1
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.24
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.13
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