TB-Profiler result

Run: SRR7645924
Summary

Run ID: SRR7645924

Sample name:

Date: 04-04-2023 19:58:46

Number of reads: 1588561

Percentage reads mapped: 94.65

Strain: 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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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 7510 p.His70Arg missense_variant 0.55 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761089 p.Ser428Thr missense_variant 0.1 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.97 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.72 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.19 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
ald 3086947 c.130dupG frameshift_variant 0.36 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247402 p.Ser297Ala missense_variant 0.88 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 7581 p.Asp94Ser missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.97
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoC 763621 c.252C>T synonymous_variant 0.12
rpoC 763633 c.264T>C synonymous_variant 0.12
rpoC 763636 c.267T>C synonymous_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.12
rpoC 763648 c.279C>G synonymous_variant 0.13
rpoC 763652 p.Ile95Leu missense_variant 0.12
rpoC 763660 c.291T>C synonymous_variant 0.12
rpoC 763666 c.297G>T synonymous_variant 0.13
rpoC 763669 c.300C>G synonymous_variant 0.12
rpoC 763672 c.303C>G synonymous_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.93
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.17
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.21
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.19
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.19
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.18
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.2
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.19
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.16
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.17
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.17
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.1
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.2
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.14
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.17
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.18
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.12
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.16
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.21
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.18
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.27
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.25
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.25
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.24
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.24
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.26
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.23
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.21
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.21
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.18
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.15
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.14
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.18
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.17
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.13
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.17
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.21
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612316 c.801T>A synonymous_variant 0.11
rpoA 3878569 c.-62C>T upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0