TB-Profiler result

Run: SRR11972156
Summary

Run ID: SRR11972156

Sample name:

Date: 03-04-2023 05:30:06

Number of reads: 531050

Percentage reads mapped: 99.04

Strain: lineage1.1.2

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 1.0
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 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 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576459 p.Ala371Asp missense_variant 0.14
rpoB 759820 p.Arg5His missense_variant 0.12
rpoB 760137 p.Ala111Ser missense_variant 0.17
rpoB 762131 c.2325C>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763084 p.Arg1093His missense_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764197 c.828G>A synonymous_variant 0.22
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 767160 p.Ile1264Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 779184 c.-704C>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406640 p.Thr234Ile missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.13
rrl 1473802 n.145C>T non_coding_transcript_exon_variant 0.95
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
rpsA 1833922 p.Lys127Asn missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102147 p.Arg299Gln missense_variant 0.13
ndh 2102595 p.Arg150Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154803 p.Leu437Met missense_variant 0.11
PPE35 2167833 p.Leu927Arg missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289882 c.-641C>T upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518535 p.Ala141Thr missense_variant 1.0
eis 2714921 p.His138Asn missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746599 c.979_999delCGGGCCGGCTTTGCCGCCGTC conservative_inframe_deletion 0.15
folC 2746628 p.Asp324Val missense_variant 0.17
ribD 2987330 c.492G>A synonymous_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087714 p.Ala299Ser missense_variant 0.14
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 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612945 p.Ile58Val missense_variant 0.15
rpoA 3877985 p.Thr175Ala missense_variant 0.14
clpC1 4039984 p.Thr241Ala missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241612 p.Thr584Pro missense_variant 0.13
embC 4242101 p.Lys747Gln missense_variant 0.12
embC 4242193 c.2331G>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242976 c.-257G>T upstream_gene_variant 0.2
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248652 p.Phe713Leu missense_variant 0.12
aftB 4268349 p.Arg163Leu missense_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327396 c.-153A>T upstream_gene_variant 0.13
ethA 4327827 c.-354A>G upstream_gene_variant 0.29
ethA 4327836 c.-363G>A upstream_gene_variant 1.0
whiB6 4338441 p.Tyr27* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338707 c.-186A>G upstream_gene_variant 0.1
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0