TB-Profiler result

Run: SRR1172171
Summary

Run ID: SRR1172171

Sample name:

Date: 03-04-2023 02:58:19

Number of reads: 2428233

Percentage reads mapped: 88.21

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 7582 p.Asp94Gly missense_variant 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.57 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.79 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.23
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.24
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.24
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.25
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.41
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.37
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.37
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.51
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.53
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.62
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.52
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.53
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.53
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.5
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.39
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.41
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.42
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.25
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.24
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.24
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.15
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.44
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.48
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.46
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.49
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.49
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.5
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.42
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.57
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.58
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.58
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.53
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.49
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.14
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.13
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.16
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.11
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.11
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.1
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.12
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.53
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.62
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.61
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.63
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.62
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.69
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.66
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.68
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.68
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.24
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326113 p.Pro454Leu missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0