TB-Profiler result

Run: SRR10397238
Summary

Run ID: SRR10397238

Sample name:

Date: 02-04-2023 17:38:18

Number of reads: 2527666

Percentage reads mapped: 99.58

Strain: lineage4.3.3;lineage4.2.1

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 0.39
lineage4.2 Euro-American H;T;LAM None 0.61
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.58
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.4
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 7582 p.Asp94Ala missense_variant 0.31 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.39 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.43 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.33 kanamycin, amikacin
ald 3087252 c.436_437dupGC frameshift_variant 0.36 cycloserine
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol
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 0.31
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.64
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576482 p.Val379Leu missense_variant 0.14
rpoB 761032 p.Gln409Arg missense_variant 0.52
rpoC 764995 c.1626C>G synonymous_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302901 c.-30G>T upstream_gene_variant 0.63
fbiC 1303095 c.165G>A synonymous_variant 0.43
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.55
rrl 1476222 n.2565A>C non_coding_transcript_exon_variant 0.61
rpsA 1834836 p.Met432Thr missense_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.39
PPE35 2169879 p.Phe245Cys missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.36
ahpC 2726142 c.-51G>A upstream_gene_variant 0.42
folC 2746340 p.Ala420Val missense_variant 0.37
ribD 2987502 p.Gly222Ser missense_variant 0.43
thyA 3073868 p.Thr202Ala missense_variant 0.39
ald 3086742 c.-78A>C upstream_gene_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612696 p.Arg141Gly missense_variant 0.66
clpC1 4038287 c.2418C>T synonymous_variant 0.37
clpC1 4038968 c.1737G>A synonymous_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.56
ethA 4326593 p.Cys294Tyr missense_variant 0.46
ethA 4328376 c.-903G>C upstream_gene_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.48