TB-Profiler result

Run: SRR9971090
Summary

Run ID: SRR9971090

Sample name:

Date: 04-04-2023 23:10:41

Number of reads: 6588333

Percentage reads mapped: 96.14

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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_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 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.99
rpoC 766992 p.Met1208Thr missense_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 1472530 n.685G>A non_coding_transcript_exon_variant 0.15
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.14
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.14
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.15
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.15
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.16
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.17
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.16
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.16
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.15
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.14
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.14
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.14
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.13
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.14
rrl 1473895 n.238C>A non_coding_transcript_exon_variant 0.12
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.2
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.22
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.22
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.22
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.29
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.33
rrl 1475671 n.2014A>G non_coding_transcript_exon_variant 0.14
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.31
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.16
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.19
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.17
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.19
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.13
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.11
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.45
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
embB 4246584 p.Arg24Pro missense_variant 0.31
ethA 4327546 c.-73T>C upstream_gene_variant 1.0
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