TB-Profiler result

Run: ERR025437
Summary

Run ID: ERR025437

Sample name:

Date: 31-03-2023 08:16:47

Number of reads: 754225

Percentage reads mapped: 99.27

Strain: lineage4.2.2;lineage4.1.2;lineage2.2.2;lineage1.2.1.2.1

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
lineage2 East-Asian Beijing RD105 0.06
lineage4 Euro-American LAM;T;S;X;H None 0.29
lineage1 Indo-Oceanic EAI RD239 0.64
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.06
lineage4.1.2 Euro-American T;H None 0.1
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.05
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.59
lineage1.2.1.2 Indo-Oceanic NA RD239 0.65
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.62
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 781822 p.Lys88Arg missense_variant 0.1 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.3 kanamycin
ethA 4326130 c.1343delA frameshift_variant 0.36 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 5716 p.Lys159Asn missense_variant 0.11
gyrB 6112 p.Met291Ile missense_variant 0.74
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.61
gyrA 9143 c.1842T>C synonymous_variant 0.31
gyrA 9260 c.1959G>C synonymous_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490987 p.Leu69Val missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.78
mshA 575368 c.21T>C synonymous_variant 0.5
mshA 575442 p.Gly32Glu missense_variant 0.78
mshA 576077 c.730C>T synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.78
rpoC 763531 c.162G>C synonymous_variant 0.65
rpoC 763884 p.Ala172Val missense_variant 0.67
rpoC 763886 c.517C>A synonymous_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 777399 p.Thr361Arg missense_variant 0.29
mmpS5 778743 p.Val55Met missense_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.18
Rv1258c 1406312 c.1029T>C synonymous_variant 0.46
embR 1417019 p.Cys110Tyr missense_variant 0.5
atpE 1460907 c.-138T>C upstream_gene_variant 0.31
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.33
inhA 1674162 c.-40C>T upstream_gene_variant 0.26
rpsA 1833909 p.Asp123Ala missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.83
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 0.58
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289524 c.-283C>T upstream_gene_variant 0.67
kasA 2518132 c.18C>T synonymous_variant 0.37
kasA 2519048 p.Gly312Ser missense_variant 0.57
eis 2715424 c.-92C>G upstream_gene_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57
pepQ 2860381 p.Gln13Leu missense_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.58
Rv3083 3448714 p.Asp71His missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.76
fprA 3475159 p.Asn385Asp missense_variant 0.59
whiB7 3568488 c.191delG frameshift_variant 0.68
fbiB 3640557 c.-978T>C upstream_gene_variant 0.6
rpoA 3878238 p.Asp90Glu missense_variant 0.38
clpC1 4039932 p.Gly258Val missense_variant 0.32
clpC1 4040517 p.Val63Ala missense_variant 0.76
embC 4240646 p.Phe262Val missense_variant 0.56
embC 4240671 p.Thr270Ile missense_variant 0.33
embC 4241042 p.Asn394Asp missense_variant 0.71
embC 4241456 p.Ala532Pro missense_variant 0.38
embC 4242369 p.Arg836Pro missense_variant 0.25
embC 4242425 p.Arg855Gly missense_variant 0.22
embC 4242476 p.Pro872Ala missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.13
embC 4242822 p.Val987Gly missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 0.18
embA 4243580 c.348G>A synonymous_variant 0.62
embA 4244420 c.1188G>C synonymous_variant 0.5
embA 4245969 p.Pro913Ser missense_variant 0.59
embB 4247578 c.1065G>A synonymous_variant 0.36
embB 4247646 p.Glu378Ala missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.27
ubiA 4269387 p.Glu149Asp missense_variant 0.65
ubiA 4269529 p.Ala102Gly missense_variant 0.3
aftB 4269606 c.-770T>C upstream_gene_variant 0.69
ubiA 4269864 c.-32delG upstream_gene_variant 0.46
whiB6 4338361 p.Arg54Gln missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.58
gid 4407588 c.615A>G synonymous_variant 0.56
gid 4407873 c.330G>T synonymous_variant 0.82
gid 4407927 p.Glu92Asp missense_variant 0.12