TB-Profiler result

Run: SRR12199473

Summary

Run ID: SRR12199473

Sample name:

Date: 03-04-2023 06:42:34

Number of reads: 561798

Percentage reads mapped: 98.12

Strain: lineage1.2.1.2.1

Drug-resistance: Sensitive


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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
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.99
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
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 1.0
gyrB 6314 p.Ser359Pro missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9256 p.Asn652Ser missense_variant 0.12
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9454 p.Arg718Leu missense_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.42
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491748 p.Glu322Asp missense_variant 0.12
mshA 575352 p.Ala2Val missense_variant 0.33
mshA 575368 c.21T>C synonymous_variant 1.0
rpoB 760553 c.747C>T synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764846 p.Glu493* stop_gained 0.12
rpoC 766970 p.Ala1201Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777562 p.Ala307Thr missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474452 n.795C>A non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.11
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>A non_coding_transcript_exon_variant 0.13
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.17
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674985 p.Gly262Cys missense_variant 0.12
rpsA 1833916 c.375C>T synonymous_variant 1.0
rpsA 1834663 c.1122C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.22
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 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 0.93
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747014 c.585C>G synonymous_variant 0.13
folC 2747430 c.169C>T synonymous_variant 0.2
ribD 2986898 c.60G>A synonymous_variant 1.0
thyX 3067867 p.Thr27Pro missense_variant 0.22
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 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475126 p.Asp374Tyr missense_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 0.89
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612368 p.Thr250Lys missense_variant 0.33
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3641346 c.-189C>T upstream_gene_variant 0.18
fbiA 3641525 p.Gly328Val missense_variant 0.29
fbiB 3641860 p.Asp109Gly missense_variant 0.22
alr 3841539 c.-119C>T upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044001 p.Asp94Gly missense_variant 0.12
panD 4044286 c.-5A>G upstream_gene_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243423 p.Ser64Phe missense_variant 0.11
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245963 p.Val911Leu missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246191 p.Phe987Leu missense_variant 0.18
embA 4246468 p.Ile1079Thr missense_variant 0.11
embB 4246878 p.Arg122His missense_variant 0.14
embB 4246881 p.Val123Gly missense_variant 0.14
embB 4246885 c.372C>T synonymous_variant 0.14
embB 4246893 p.Asp127Ala missense_variant 0.14
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326626 p.Gly283Val missense_variant 0.17
ethR 4326640 c.-909C>A upstream_gene_variant 0.18
ethA 4326671 p.Ile268Thr missense_variant 0.2
ethA 4327023 p.Phe151Leu missense_variant 0.1
ethA 4327241 p.Gly78Asp missense_variant 0.12
whiB6 4338361 p.Arg54Gln missense_variant 1.0
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 4407873 c.330G>T synonymous_variant 1.0