TB-Profiler result

Run: ERR7821210
Summary

Run ID: ERR7821210

Sample name:

Date: 02-04-2023 06:25:06

Number of reads: 1051157

Percentage reads mapped: 93.79

Strain: lineage1.2.2.1

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 0.97
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7906 p.Phe202Ser missense_variant 0.12
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 491060 p.Met93Thr missense_variant 1.0
fgd1 491603 p.Ala274Glu missense_variant 0.13
fgd1 491610 c.828A>C synonymous_variant 0.15
fgd1 491616 c.834A>G synonymous_variant 0.14
fgd1 491620 p.Ile280Val missense_variant 0.14
fgd1 491643 c.861G>C synonymous_variant 0.15
fgd1 491649 c.867C>T synonymous_variant 0.15
fgd1 491658 c.876A>G synonymous_variant 0.17
fgd1 491661 c.879C>G synonymous_variant 0.17
fgd1 491673 c.891A>C synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576089 p.Ala254Gly missense_variant 0.33
ccsA 620659 p.Arg257Cys missense_variant 1.0
rpoC 762410 c.-960T>C upstream_gene_variant 0.12
rpoC 762416 c.-954A>G upstream_gene_variant 0.12
rpoB 762750 p.Leu982Met missense_variant 0.12
rpoB 762785 p.Asp993Glu missense_variant 0.16
rpoC 762788 c.-582G>C upstream_gene_variant 0.15
rpoB 762789 p.Leu995Met missense_variant 0.15
rpoB 762795 p.Asp997Asn missense_variant 0.15
rpoB 762799 p.Ala998Gly missense_variant 0.15
rpoC 762812 c.-558C>G upstream_gene_variant 0.14
rpoB 762813 p.Met1003Val missense_variant 0.14
rpoC 762818 c.-552C>G upstream_gene_variant 0.14
rpoC 762827 c.-543G>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765580 c.2211G>C synonymous_variant 0.14
rpoC 765583 c.2214G>C synonymous_variant 0.14
rpoC 765613 p.His748Gln missense_variant 0.17
rpoC 765625 c.2256C>G synonymous_variant 0.14
rpoC 765628 c.2259G>C synonymous_variant 0.14
rpoC 765658 c.2289C>T synonymous_variant 0.18
rpoC 765886 c.2517C>G synonymous_variant 0.19
rpoC 765934 c.2565C>T synonymous_variant 0.16
rpoC 765937 c.2568T>C synonymous_variant 0.16
rpoC 765982 c.2613C>G synonymous_variant 0.13
rpoC 765994 c.2625A>T synonymous_variant 0.14
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.12
rpoC 766021 c.2652G>C synonymous_variant 0.14
rpoC 766027 c.2658G>C synonymous_variant 0.14
rpoC 766843 c.3474T>C synonymous_variant 0.12
rpoC 766921 c.3552G>C synonymous_variant 0.12
rpoC 766924 p.Glu1185Asp missense_variant 0.12
rpoC 766933 c.3564A>G synonymous_variant 0.12
rpoC 767098 c.3729T>C synonymous_variant 0.12
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
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.13
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.12
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.15
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.15
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.16
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917893 c.-47G>C upstream_gene_variant 0.11
tlyA 1917897 c.-43T>C upstream_gene_variant 0.12
tlyA 1917900 c.-40T>C upstream_gene_variant 0.12
tlyA 1917908 c.-32C>G upstream_gene_variant 0.12
tlyA 1917929 c.-11T>C upstream_gene_variant 0.12
tlyA 1917943 p.Ala2Ser missense_variant 0.13
tlyA 1917951 c.12T>C synonymous_variant 0.13
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518162 c.48G>A synonymous_variant 0.12
kasA 2518174 c.60A>G synonymous_variant 0.12
kasA 2518220 c.106C>T synonymous_variant 0.12
kasA 2518348 c.234A>T synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
thyX 3068115 c.-170C>T upstream_gene_variant 1.0
thyA 3073977 c.495A>G synonymous_variant 0.12
thyA 3073989 c.483T>C synonymous_variant 0.15
thyA 3073997 c.475C>T synonymous_variant 0.14
thyA 3073998 c.474G>A synonymous_variant 0.14
thyA 3074001 c.471C>G synonymous_variant 0.14
thyA 3074004 p.Asp156Gly missense_variant 0.14
thyA 3074010 c.462C>G synonymous_variant 0.2
thyA 3074031 c.441T>C synonymous_variant 0.27
thyA 3074034 c.438T>C synonymous_variant 0.75
thyA 3074037 c.435C>G synonymous_variant 0.3
thyA 3074053 p.Arg140Gln missense_variant 0.22
thyA 3074056 p.Glu139Pro missense_variant 0.2
thyA 3074076 c.396C>G synonymous_variant 0.22
thyA 3074120 c.352T>C synonymous_variant 0.14
thyA 3074121 p.Asp117Glu missense_variant 0.13
thyA 3074127 c.345G>C synonymous_variant 0.13
thyA 3074130 c.342G>C synonymous_variant 0.13
thyA 3074172 c.300G>C synonymous_variant 0.12
thyA 3074220 c.252A>T synonymous_variant 0.17
thyA 3074244 c.228A>T synonymous_variant 0.17
thyA 3074262 p.Gly70Ala missense_variant 0.16
thyA 3074267 p.Ile69Val missense_variant 0.14
thyA 3074268 c.204T>C synonymous_variant 0.14
thyA 3074285 c.187T>C synonymous_variant 0.14
thyA 3074286 c.186T>C synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_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 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878169 c.339G>T synonymous_variant 0.12
rpoA 3878193 c.315T>C synonymous_variant 0.14
rpoA 3878247 c.261G>C synonymous_variant 0.13
rpoA 3878250 c.258C>G synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244904 p.Val558Ile missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.23
embB 4246556 p.Ala15Pro missense_variant 0.23
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247024 p.Pro171Ala missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_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