TB-Profiler result

Run: SRR19428586
Summary

Run ID: SRR19428586

Sample name:

Date: 03-04-2023 21:41:09

Number of reads: 294932

Percentage reads mapped: 99.35

Strain: lineage4.3.4

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
lineage4 Euro-American LAM;T;S;X;H None 0.96
lineage4.3.4 Euro-American (LAM) LAM RD174 0.78
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
katG 2156089 c.22delA frameshift_variant 0.12 isoniazid
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 5075 c.-165C>T upstream_gene_variant 0.19
gyrA 6817 c.-485G>A upstream_gene_variant 0.59
gyrA 7268 c.-34C>T upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8280 c.980delT frameshift_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491248 p.Arg156Gly missense_variant 0.17
fgd1 491362 p.Cys194Arg missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.41
ccsA 619940 p.Ala17Glu missense_variant 0.22
rpoB 760906 p.Phe367Ser missense_variant 0.18
rpoB 761184 p.Glu460* stop_gained 0.18
rpoB 761658 p.Pro618Thr missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
rpoC 763552 c.183C>T synonymous_variant 0.19
rpoC 763884 p.Ala172Val missense_variant 0.2
rpoC 763886 c.517C>A synonymous_variant 0.2
rpoC 764797 c.1428G>T synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.69
rpoC 765668 p.His767Asn missense_variant 0.17
rpoC 765783 p.Ser805Tyr missense_variant 0.14
rpoC 765806 p.Gln813Lys missense_variant 0.14
rpoC 766242 p.Thr958Ile missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.29
mmpL5 777560 c.921C>A synonymous_variant 0.33
mmpS5 778599 p.Ile103Phe missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781626 p.Ala23Ser missense_variant 0.15
rpsL 781828 p.Leu90Pro missense_variant 0.11
fbiC 1304557 p.Glu543* stop_gained 0.15
fbiC 1304643 p.Lys571Asn missense_variant 0.13
fbiC 1304946 c.2016G>A synonymous_variant 0.14
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 1.0
Rv1258c 1406512 p.Gly277Trp missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 0.33
embR 1417241 p.Arg36Leu missense_variant 0.12
embR 1417523 c.-177delG upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471667 n.-179A>G upstream_gene_variant 0.29
rrs 1472320 n.475G>A non_coding_transcript_exon_variant 0.2
rrs 1472355 n.510C>A non_coding_transcript_exon_variant 0.25
rrl 1473955 n.298G>T non_coding_transcript_exon_variant 0.2
rrl 1474091 n.434C>A non_coding_transcript_exon_variant 0.18
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12
rrl 1475097 n.1440G>T non_coding_transcript_exon_variant 0.22
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.29
inhA 1674505 p.Gly102Trp missense_variant 0.25
inhA 1674518 p.Asn106Ile missense_variant 0.22
inhA 1674774 c.573A>G synonymous_variant 0.15
rpsA 1834100 p.Arg187Ser missense_variant 0.13
rpsA 1834247 p.His236Asn missense_variant 0.11
rpsA 1834355 p.Val272Ile missense_variant 0.13
rpsA 1834435 c.894G>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918692 p.Leu251Phe missense_variant 0.1
ndh 2101747 c.1296C>A synonymous_variant 0.13
ndh 2101808 p.Thr412Asn missense_variant 0.14
ndh 2102240 p.Arg268His missense_variant 0.62
ndh 2102614 c.429C>T synonymous_variant 0.14
katG 2154128 p.Leu662Ile missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 0.17
katG 2154852 p.Met420Ile missense_variant 0.15
katG 2155976 p.Lys46Glu missense_variant 0.11
PPE35 2168339 c.2274A>G synonymous_variant 0.29
PPE35 2168603 c.2010C>A synonymous_variant 0.12
PPE35 2168705 c.1908T>A synonymous_variant 0.12
PPE35 2168742 p.Gly624Asp missense_variant 0.29
PPE35 2169048 p.Ile522Asn missense_variant 0.12
PPE35 2170593 p.Pro7Leu missense_variant 0.14
Rv1979c 2222286 c.879G>T synonymous_variant 0.15
Rv1979c 2222291 p.Ala292Ser missense_variant 0.15
Rv1979c 2222340 p.Met275Ile missense_variant 0.13
Rv1979c 2222468 p.Thr233Ala missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288758 p.Gly162Cys missense_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 0.17
eis 2715522 c.-190G>A upstream_gene_variant 0.4
folC 2746438 c.1161G>T synonymous_variant 0.17
folC 2747666 c.-68A>G upstream_gene_variant 0.2
Rv2752c 3065305 p.Ala296Glu missense_variant 0.15
thyX 3067515 p.Ser144Ile missense_variant 0.12
thyX 3067675 p.His91Tyr missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 0.79
thyA 3074660 c.-189C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339156 p.Ile13Met missense_variant 0.11
fbiD 3339200 c.85delG frameshift_variant 0.12
Rv3083 3449337 c.834C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.22
fprA 3474997 p.Gly331Arg missense_variant 0.25
whiB7 3568762 c.-83G>T upstream_gene_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 0.74
fbiA 3640757 p.Gly72Val missense_variant 0.22
fbiA 3640921 p.Gln127Lys missense_variant 0.14
fbiA 3641260 p.Ile240Val missense_variant 0.17
fbiB 3641755 p.Arg74Leu missense_variant 0.18
fbiB 3642524 c.990G>C synonymous_variant 0.2
rpoA 3877791 c.717C>A synonymous_variant 0.29
rpoA 3878397 c.111G>A synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.7
clpC1 4038330 p.Glu792Gly missense_variant 0.1
clpC1 4038350 c.2355C>A synonymous_variant 0.14
clpC1 4038865 p.Val614Leu missense_variant 0.33
clpC1 4038872 c.1833C>G synonymous_variant 0.25
clpC1 4039058 p.Phe549Leu missense_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 0.44
clpC1 4040719 c.-15A>G upstream_gene_variant 0.5
embC 4239746 c.-117C>A upstream_gene_variant 0.13
embC 4239763 c.-100C>T upstream_gene_variant 0.33
embC 4240350 p.Arg163Leu missense_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 0.17
embC 4241077 c.1215C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243076 p.Pro1072Ser missense_variant 0.17
embA 4243782 p.Gly184Trp missense_variant 0.14
embA 4244030 c.798C>A synonymous_variant 0.12
embA 4244081 c.849C>T synonymous_variant 0.13
embA 4245670 p.Ala813Gly missense_variant 0.44
embA 4245969 p.Pro913Ser missense_variant 0.33
embA 4246069 p.Pro946Gln missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4247061 p.Pro183Gln missense_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 0.31
embB 4248324 p.Ala604Val missense_variant 0.12
embB 4248686 p.Gly725Trp missense_variant 0.14
embB 4249206 p.Val898Glu missense_variant 0.12
aftB 4268347 p.Ala164Ser missense_variant 0.14
aftB 4268640 p.Leu66Pro missense_variant 0.17
aftB 4268783 c.54C>A synonymous_variant 0.13
ubiA 4269019 p.Gly272Val missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.28
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ethA 4326061 c.1413C>A synonymous_variant 0.12
ethA 4326439 p.Asn345Lys missense_variant 0.21
ethA 4326611 p.Pro288His missense_variant 0.15
ethA 4327397 p.Arg26Leu missense_variant 0.13
whiB6 4338203 p.Arg107Cys missense_variant 0.4
whiB6 4338489 c.33C>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.25
gid 4407848 p.Ala119Thr missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.21
gid 4408156 p.Leu16Arg missense_variant 0.79
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0