TB-Profiler result

Run: SRR12199442
Summary

Run ID: SRR12199442

Sample name:

Date: 03-04-2023 06:40:56

Number of reads: 607536

Percentage reads mapped: 98.45

Strain: lineage1.2.2

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 0.89
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.05
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.33 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.35 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 6112 p.Met291Ile missense_variant 0.8
gyrA 7268 c.-34C>T upstream_gene_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.89
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 0.62
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759776 c.-31T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763083 p.Arg1093Ser missense_variant 0.33
rpoC 763884 p.Ala172Val missense_variant 0.91
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 0.86
atpE 1460907 c.-138T>C upstream_gene_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.4
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472682 n.837T>G non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.29
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.25
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.25
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.3
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.22
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.22
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.22
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.2
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.22
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.3
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.22
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.22
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.2
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.4
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.5
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.67
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.2
fabG1 1673361 c.-79C>G upstream_gene_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.45
inhA 1674162 c.-40C>T upstream_gene_variant 0.5
inhA 1674880 p.Pro227Thr missense_variant 0.25
rpsA 1833916 c.375C>T synonymous_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.5
PPE35 2169901 p.Gly238Trp missense_variant 0.18
PPE35 2169948 p.Asn222Ser missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
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 0.9
kasA 2519048 p.Gly312Ser missense_variant 0.21
eis 2714124 c.1209A>G stop_lost&splice_region_variant 0.2
ahpC 2726035 c.-158G>C upstream_gene_variant 0.16
ahpC 2726051 c.-142G>A upstream_gene_variant 0.8
ribD 2986898 c.60G>A synonymous_variant 0.8
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.83
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.88
fprA 3475159 p.Asn385Asp missense_variant 0.66
whiB7 3568488 c.191delG frameshift_variant 0.83
fbiB 3640557 c.-978T>C upstream_gene_variant 0.83
alr 3840689 c.732C>T synonymous_variant 0.12
clpC1 4039508 c.1197G>C synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.89
embC 4240671 p.Thr270Ile missense_variant 0.83
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 0.56
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.8
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 0.5
embB 4247646 p.Glu378Ala missense_variant 0.75
aftB 4267647 p.Asp397Gly missense_variant 0.3
aftB 4267881 p.Gly319Val missense_variant 0.4
aftB 4268468 c.369G>C synonymous_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 0.83
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
ubiA 4269864 c.-32delG upstream_gene_variant 0.64
ethA 4326881 p.Gly198Ala missense_variant 0.22
whiB6 4338203 p.Arg107Cys missense_variant 0.15
whiB6 4338361 p.Arg54Gln missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.29
gid 4407873 c.330G>T synonymous_variant 0.8
gid 4407927 p.Glu92Asp missense_variant 0.29