TB-Profiler result

Run: ERR4821880
Summary

Run ID: ERR4821880

Sample name:

Date: 01-04-2023 17:30:23

Number of reads: 392756

Percentage reads mapped: 82.02

Strain: lineage1.1.2

Drug-resistance: HR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.95
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
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
ethA 4326419 c.1054delG frameshift_variant 0.83 ethionamide, 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
gyrB 5500 c.261C>T synonymous_variant 0.2
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7882 p.Leu194Pro missense_variant 0.17
gyrA 8452 p.Ala384Val missense_variant 0.73
gyrA 9143 c.1842T>C synonymous_variant 0.92
gyrA 9171 p.Val624Leu missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490811 p.Ala10Val missense_variant 0.89
fgd1 490819 p.Glu13Lys missense_variant 0.25
fgd1 491426 p.Ala215Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576376 c.1029G>A synonymous_variant 0.12
rpoB 761722 p.Glu639Gly missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765988 c.2619G>A synonymous_variant 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.75
mmpL5 776868 p.Arg538Gln missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781904 p.Ser115Arg missense_variant 0.29
fbiC 1305229 p.Arg767Cys missense_variant 0.33
Rv1258c 1406365 p.Gly326* stop_gained 0.15
Rv1258c 1406479 p.Arg288Ser missense_variant 0.2
Rv1258c 1406797 p.Gly182Arg missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461049 p.Asp2Gly missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.5
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 1.0
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 1.0
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 1.0
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.86
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472620 n.775A>G non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.83
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.83
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.92
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.92
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.93
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.86
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.67
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
fabG1 1673343 c.-96delC upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918033 p.Val32Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155917 c.195C>A synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.86
Rv1979c 2221791 c.1374G>T synonymous_variant 0.17
Rv1979c 2221909 p.Leu419Pro missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.93
kasA 2518183 c.69G>A synonymous_variant 0.12
eis 2714807 c.525delT frameshift_variant 0.12
eis 2714990 p.Val115Ile missense_variant 0.12
eis 2715005 c.327delC frameshift_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86
ahpC 2726468 c.276G>A synonymous_variant 0.9
folC 2746237 c.1362G>C synonymous_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064715 p.His493Asn missense_variant 0.29
Rv2752c 3065780 p.Val138Leu missense_variant 0.2
thyX 3067491 p.Ala152Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448631 p.Gly43Asp missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448882 c.382dupA frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.89
fprA 3475159 p.Asn385Asp missense_variant 0.83
fprA 3475313 p.Pro436Gln missense_variant 0.4
Rv3236c 3612223 c.894C>G synonymous_variant 1.0
Rv3236c 3612495 c.622C>A synonymous_variant 0.4
Rv3236c 3612581 p.Leu179Pro missense_variant 1.0
Rv3236c 3612942 p.Ala59Thr missense_variant 0.29
fbiA 3641341 p.Ser267Pro missense_variant 0.14
fbiB 3642512 c.978G>A synonymous_variant 0.12
clpC1 4038566 c.2139C>A synonymous_variant 0.4
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239761 c.-102C>T upstream_gene_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.75
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244873 c.1641C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248083 p.Arg524Cys missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4270027 c.-194C>T upstream_gene_variant 0.12
ethA 4327451 p.Val8Asp missense_variant 0.29
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.8
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0