TB-Profiler result

Run: ERR4819839
Summary

Run ID: ERR4819839

Sample name:

Date: 01-04-2023 16:19:59

Number of reads: 200587

Percentage reads mapped: 98.03

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
lineage1.1 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 5311 c.72G>A synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6642 p.Lys468Arg missense_variant 0.33
gyrB 6752 p.Ile505Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7612 p.Ser104Leu missense_variant 0.4
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9233 c.1932C>G synonymous_variant 0.2
gyrA 9242 c.1941A>G synonymous_variant 0.22
gyrA 9251 c.1950G>C synonymous_variant 0.29
gyrA 9252 p.Val651Ile missense_variant 0.29
gyrA 9263 c.1962C>T synonymous_variant 0.33
gyrA 9284 c.1983T>C synonymous_variant 0.22
gyrA 9296 c.1995T>C synonymous_variant 0.2
gyrA 9299 c.1998G>C synonymous_variant 0.25
gyrA 9300 p.Ala667Ser missense_variant 0.25
gyrA 9304 p.Gly668Glu missense_variant 1.0
gyrA 9308 p.Asp669Glu missense_variant 0.25
gyrA 9323 c.2022C>G synonymous_variant 0.25
gyrA 9329 c.2028C>G synonymous_variant 0.29
gyrA 9508 p.Ala736Val missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
ccsA 620503 p.Glu205Lys missense_variant 0.25
rpoB 760119 p.Arg105Cys missense_variant 0.29
rpoB 760261 p.Pro152Leu missense_variant 0.22
rpoB 760490 c.684C>T synonymous_variant 1.0
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 765171 p.Pro601Leu missense_variant 1.0
rpoC 766749 p.Pro1127Leu missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778046 c.-944C>T upstream_gene_variant 0.12
mmpL5 778056 p.Ser142Thr missense_variant 0.14
mmpR5 778061 c.-929C>T upstream_gene_variant 0.15
mmpL5 778064 p.Ala139Ser missense_variant 0.17
mmpL5 778072 p.Thr137Ala missense_variant 0.18
mmpR5 778073 c.-917G>C upstream_gene_variant 0.18
mmpR5 778082 c.-908T>C upstream_gene_variant 0.22
mmpR5 778088 c.-902C>G upstream_gene_variant 0.22
mmpL5 779148 c.-668C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302809 c.-122A>G upstream_gene_variant 0.5
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673392 c.-48G>T upstream_gene_variant 0.17
fabG1 1673608 p.Gly57Ser missense_variant 0.5
inhA 1674311 p.Val37Ala missense_variant 0.67
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169479 c.1134C>T synonymous_variant 0.22
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
eis 2714573 c.759delG frameshift_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747038 c.561C>T synonymous_variant 0.25
pepQ 2859495 p.Ile308Met missense_variant 0.67
ribD 2986663 c.-176C>T upstream_gene_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074595 c.-124C>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086955 p.Thr46Ala missense_variant 0.33
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474207 c.201C>T synonymous_variant 0.29
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612005 p.Arg371His missense_variant 0.29
fbiA 3640582 p.Arg14Ser missense_variant 0.18
fbiB 3642320 c.786C>T synonymous_variant 0.25
fbiB 3642612 p.Tyr360His missense_variant 0.5
alr 3840856 c.565C>A synonymous_variant 0.33
rpoA 3878372 p.Ile46Phe missense_variant 0.33
clpC1 4039331 c.1374C>A synonymous_variant 0.22
clpC1 4039428 p.Glu426Val missense_variant 0.67
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040669 c.36C>T synonymous_variant 0.25
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 4243848 p.Val206Met missense_variant 1.0
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269961 c.-128C>G upstream_gene_variant 0.4
ethA 4328302 c.-829C>G upstream_gene_variant 0.18
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 4407701 p.His168Tyr missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408009 p.Val65Ala missense_variant 0.18