TB-Profiler result

Run: ERR4596929
Summary

Run ID: ERR4596929

Sample name:

Date: 01-04-2023 06:30:07

Number of reads: 6052992

Percentage reads mapped: 85.17

Strain: lineage4.2.2.2;lineage3

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
lineage3 East-African-Indian CAS RD750 0.33
lineage4 Euro-American LAM;T;S;X;H None 0.66
lineage4.2 Euro-American H;T;LAM None 0.69
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.67
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.66
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 761100 p.Gln432Glu missense_variant 0.69 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.58 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.4 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.73 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.64 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 8131 p.Gln277Arg missense_variant 0.35
gyrA 8688 p.Ala463Ser missense_variant 0.63
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.37
mshA 576077 c.730C>T synonymous_variant 0.72
mshA 576108 p.Ala254Gly missense_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 0.36
rpoB 761248 p.Glu481Ala missense_variant 0.67
rpoB 761489 c.1683G>A synonymous_variant 0.73
rpoC 762434 c.-936T>G upstream_gene_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
rpsL 781382 c.-178T>C upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.1
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.24
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.23
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.3
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.37
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.25
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.32
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.32
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.24
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.21
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.21
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.26
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.41
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.41
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.34
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.27
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.13
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.68
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.2
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.26
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.19
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.13
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.24
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.42
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.27
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.54
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.54
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.55
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.45
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.34
PPE35 2167926 p.Leu896Ser missense_variant 0.32
PPE35 2168863 c.1750C>T synonymous_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 0.55
pncA 2289047 c.195C>T synonymous_variant 0.35
pncA 2289365 c.-125delC upstream_gene_variant 0.35
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.66
ald 3086742 c.-78A>C upstream_gene_variant 0.65
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4040753 c.-49G>A upstream_gene_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 0.88
gid 4407588 c.615A>G synonymous_variant 0.34