TB-Profiler result

Run: ERR4817281
Summary

Run ID: ERR4817281

Sample name:

Date: 01-04-2023 14:54:20

Number of reads: 670840

Percentage reads mapped: 99.2

Strain: lineage1.2.2.2

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 0.78
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 8536 p.Glu412Gly missense_variant 1.0
gyrA 8673 p.Ile458Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9378 p.Met693Val missense_variant 0.11
fgd1 491087 p.Phe102Ser missense_variant 0.11
fgd1 491704 c.922C>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760434 p.Val210Ile missense_variant 0.13
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 767011 c.3642G>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778660 c.-180C>T upstream_gene_variant 0.12
mmpR5 779326 p.Glu113* stop_gained 0.14
rpsL 781370 c.-189delT upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303846 p.Phe306Leu missense_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461166 p.Arg41Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475331 n.1674G>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102366 p.Ala226Glu missense_variant 0.11
katG 2154178 p.Val645Ala missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169733 p.Asn294Asp missense_variant 0.12
Rv1979c 2221725 c.1440T>G synonymous_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222873 p.His98Asn missense_variant 0.14
Rv1979c 2223052 p.Glu38Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519083 c.969C>T synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3065588 p.Asp202Asn missense_variant 0.14
Rv2752c 3065597 c.595T>C synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087035 c.216C>T synonymous_variant 0.12
ald 3087616 p.Asp266Gly missense_variant 0.1
fbiD 3339388 p.Pro91Thr missense_variant 0.2
fbiD 3339732 c.615C>T synonymous_variant 0.23
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448791 p.Glu96Asp missense_variant 0.11
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 3612838 c.279G>T synonymous_variant 0.12
fbiB 3641822 p.Glu96Asp missense_variant 0.12
fbiB 3641935 p.Ala134Asp missense_variant 0.12
fbiB 3642407 c.873C>T synonymous_variant 0.12
alr 3840868 p.Glu185Lys missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
rpoA 3878451 c.57C>T synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040813 c.-109A>G upstream_gene_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242375 p.Arg838Gln missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>C synonymous_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249505 p.Gln998Glu missense_variant 0.11
embB 4249732 c.3219C>A synonymous_variant 0.12
aftB 4267485 p.Leu451Pro missense_variant 0.12
ubiA 4269373 p.Ser154* stop_gained 0.14
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
ethA 4327260 p.Arg72Trp missense_variant 0.11
ethA 4327887 c.-414T>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.93
whiB6 4338635 c.-114A>C upstream_gene_variant 0.94
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0