TB-Profiler result

Run: SRR11972237
Summary

Run ID: SRR11972237

Sample name:

Date: 03-04-2023 05:32:56

Number of reads: 226604

Percentage reads mapped: 99.21

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 6566 p.Ala443Thr missense_variant 0.2
gyrB 7020 p.Gly594Glu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7945 p.Thr215Asn missense_variant 0.33
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
rpoB 760741 p.Lys312Arg missense_variant 0.33
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 764966 p.Asn533Asp missense_variant 0.18
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765499 c.2130C>T synonymous_variant 0.33
rpoC 767153 p.Thr1262Ser missense_variant 0.25
rpoC 767214 p.Ala1282Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775859 p.Met874Ile missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778843 c.-363C>T upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800692 c.-117C>T upstream_gene_variant 0.25
rplC 801073 p.Ser89Thr missense_variant 0.13
fbiC 1304991 c.2061G>A synonymous_variant 0.14
fbiC 1305407 p.Ser826Leu missense_variant 1.0
fbiC 1305501 c.2571G>A splice_region_variant&stop_retained_variant 0.18
Rv1258c 1406112 p.Asp410Gly missense_variant 0.29
Rv1258c 1406354 p.Gln329His missense_variant 0.25
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
embR 1416529 c.819C>T synonymous_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417355 c.-8G>T upstream_gene_variant 0.22
atpE 1461055 p.Thr4Ile missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472334 n.489A>G non_coding_transcript_exon_variant 0.13
rrl 1474129 n.472C>A non_coding_transcript_exon_variant 0.13
rrl 1474480 n.823T>A non_coding_transcript_exon_variant 0.15
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.17
inhA 1673469 c.-733A>G upstream_gene_variant 0.22
rpsA 1834077 p.Asn179Ile missense_variant 0.15
rpsA 1834226 p.Gly229Cys missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918247 p.Arg103His missense_variant 0.25
tlyA 1918630 p.Pro231Ser missense_variant 0.29
ndh 2102156 p.Glu296Gly missense_variant 0.5
ndh 2103042 c.1A>T initiator_codon_variant 0.13
katG 2156284 c.-173C>T upstream_gene_variant 0.18
PPE35 2167814 c.2799C>T synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.43
PPE35 2169910 p.Asn235Tyr missense_variant 0.47
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170049 c.564G>A synonymous_variant 0.14
PPE35 2170547 c.66A>C synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289884 c.-643G>T upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518633 c.519G>C synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747665 c.-67T>C upstream_gene_variant 1.0
ribD 2986708 c.-131G>A upstream_gene_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065369 p.Gln275* stop_gained 0.4
thyX 3067829 c.117C>T synonymous_variant 0.29
thyA 3074097 c.375C>A synonymous_variant 0.2
thyA 3074180 c.291delA frameshift_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 c.999C>T synonymous_variant 0.4
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
whiB7 3568846 c.-167G>A upstream_gene_variant 0.13
fbiA 3641071 p.Arg177Cys missense_variant 0.33
fbiB 3641151 c.-384G>A upstream_gene_variant 0.5
alr 3840723 p.His233Arg missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.24
ddn 3987282 p.Val147Leu missense_variant 0.22
clpC1 4038439 p.Lys756Glu missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.4
clpC1 4039829 p.Leu292Ile missense_variant 0.25
clpC1 4039931 c.773delG frameshift_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240693 c.831T>C synonymous_variant 0.14
embC 4240917 p.Ala352Val missense_variant 0.25
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241069 p.Ala403Thr missense_variant 0.33
embC 4241858 p.Leu666Phe missense_variant 0.25
embC 4241934 p.Ala691Val missense_variant 0.22
embC 4242435 p.Val858Ala missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242973 p.Glu1037Asp missense_variant 0.4
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245707 p.His825Gln missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247709 p.Asn399Ser missense_variant 0.33
embB 4248537 p.Leu675Pro missense_variant 0.12
embB 4248685 c.2172C>G synonymous_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269831 c.3G>T start_lost 0.15
ubiA 4269953 c.-120C>T upstream_gene_variant 0.25
whiB6 4338224 c.297delC frameshift_variant 1.0
whiB6 4338271 p.Ser84* stop_gained 0.29
whiB6 4338334 p.Ala63Glu missense_variant 0.29
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 4407756 p.Ser149Arg missense_variant 0.25
gid 4407873 c.330G>T synonymous_variant 1.0