TB-Profiler result

Run: ERR9117838
Summary

Run ID: ERR9117838

Sample name:

Date: 02-04-2023 09:32:54

Number of reads: 1073348

Percentage reads mapped: 99.26

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
gyrB 6547 c.1310delG frameshift_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575504 p.His53Tyr missense_variant 0.17
mshA 575730 p.Gln128Pro missense_variant 0.11
ccsA 619831 c.-60T>G upstream_gene_variant 0.27
ccsA 620748 c.858T>G synonymous_variant 0.27
ccsA 620753 p.Arg288Leu missense_variant 0.14
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304419 p.Ala497Thr missense_variant 1.0
fbiC 1304474 p.Leu515Pro missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674875 p.Arg225Leu missense_variant 0.4
rpsA 1834575 p.Met345Thr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154911 p.Pro401Thr missense_variant 0.12
katG 2155845 c.267G>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290136 c.-895C>T upstream_gene_variant 1.0
pncA 2290182 c.-941G>C upstream_gene_variant 0.11
kasA 2518123 c.9G>A synonymous_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715557 c.-225C>T upstream_gene_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746828 c.771C>T synonymous_variant 0.13
pepQ 2859489 c.930C>G synonymous_variant 0.11
pepQ 2860011 p.Asp136Glu missense_variant 0.14
Rv2752c 3064558 p.Tyr545Cys missense_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064983 c.1209G>A synonymous_variant 0.12
thyX 3067208 c.738G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449178 p.Lys225Asn missense_variant 0.12
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 3612922 c.195T>G synonymous_variant 0.11
Rv3236c 3613016 p.Pro34Gln missense_variant 1.0
fbiA 3640398 c.-145G>C upstream_gene_variant 1.0
fbiB 3641921 c.387C>T synonymous_variant 0.2
alr 3841138 p.Asp95Asn missense_variant 1.0
alr 3841200 p.Ala74Gly missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240625 p.Asp255Asn missense_variant 0.14
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 4243138 c.-95C>A upstream_gene_variant 0.12
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 4246508 c.-6G>C upstream_gene_variant 0.11
embB 4247070 p.Val186Asp missense_variant 0.12
embB 4247620 c.1107G>T synonymous_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268915 c.-79C>T upstream_gene_variant 0.13
ubiA 4268941 p.Ala298Val missense_variant 0.14
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
ethA 4328392 c.-919C>A upstream_gene_variant 0.12
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
gid 4408291 c.-89C>T upstream_gene_variant 0.13