TB-Profiler result

Run: SRR11972226
Summary

Run ID: SRR11972226

Sample name:

Date: 03-04-2023 05:32:41

Number of reads: 591694

Percentage reads mapped: 99.2

Strain: lineage1.1.3.1

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 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 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 6112 p.Met291Ile missense_variant 1.0
gyrA 6436 c.-866C>T upstream_gene_variant 1.0
gyrB 7032 p.Gly598Glu missense_variant 0.15
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 8689 p.Ala463Val missense_variant 0.12
gyrA 8731 p.Gly477Glu missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491656 p.Glu292Lys missense_variant 0.12
fgd1 491687 p.Thr302Lys missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619857 c.-34C>T upstream_gene_variant 0.14
rpoB 759994 p.Arg63His missense_variant 0.12
rpoB 761275 p.Leu490Pro missense_variant 0.12
rpoB 761331 p.Pro509Ser missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764038 p.Trp223Cys missense_variant 0.13
rpoC 764981 p.Gly538Ser missense_variant 0.13
rpoC 765101 c.1732C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 767034 p.Ser1222* stop_gained 0.13
mmpL5 775621 p.Ser954Pro missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775658 p.Gln941His missense_variant 0.14
mmpL5 776048 c.2433G>A synonymous_variant 0.2
mmpL5 776080 p.Ala801Thr missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 1.0
mmpL5 778922 c.-442G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471998 n.153G>A non_coding_transcript_exon_variant 0.12
rrl 1475065 n.1408G>A non_coding_transcript_exon_variant 0.15
inhA 1674910 p.Pro237Ser missense_variant 0.12
tlyA 1917952 p.Ala5Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102170 p.Glu291Asp missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167868 c.2745A>C synonymous_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169672 p.Ser314Phe missense_variant 0.12
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 2519142 p.Leu343Pro missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746393 c.1206C>G synonymous_variant 0.18
ribD 2986864 p.Ala9Asp missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065218 p.Ser325Asn missense_variant 0.11
ald 3086645 c.-175C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448773 c.270G>A synonymous_variant 0.13
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
fbiB 3641590 p.Gly19Val missense_variant 0.12
alr 3840689 c.732C>T synonymous_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
clpC1 4038362 c.2343C>A synonymous_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 4241227 c.1365G>T synonymous_variant 0.14
embC 4241971 p.Ile703Met missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244906 c.1674C>T synonymous_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249641 p.Leu1043* stop_gained 0.15
ubiA 4269002 p.Ala278Thr missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408291 c.-89C>T upstream_gene_variant 0.13
gid 4408465 c.-263C>T upstream_gene_variant 0.18
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0