TB-Profiler result

Run: SRR11972238
Summary

Run ID: SRR11972238

Sample name:

Date: 03-04-2023 05:33:05

Number of reads: 267950

Percentage reads mapped: 99.19

Strain: lineage1.1.2

Drug-resistance: Other

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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
lineage1.1.2 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
pncA 2289186 p.Leu19Pro missense_variant 0.25 pyrazinamide
folC 2747381 p.Asn73Ser missense_variant 0.33 para-aminosalicylic_acid
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
gyrA 6688 c.-614C>T upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7921 p.Asn207Ile missense_variant 0.15
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
ccsA 620394 c.504G>A synonymous_variant 0.2
ccsA 620675 p.Asp262Gly missense_variant 0.14
rpoB 759611 c.-195delC upstream_gene_variant 0.12
rpoC 762407 c.-963G>A upstream_gene_variant 0.22
rpoB 762897 p.Val1031Leu missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763048 c.3243delG frameshift_variant 0.33
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 766717 c.3348C>T synonymous_variant 0.2
rpoC 766740 p.Val1124Ala missense_variant 0.22
rpoC 767160 p.Ile1264Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775771 p.Ala904Thr missense_variant 0.67
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777105 p.Ser459Leu missense_variant 0.22
mmpL5 778359 p.Val41Ala missense_variant 0.25
mmpS5 778536 p.Asp124Asn missense_variant 0.22
mmpL5 778771 c.-291C>T upstream_gene_variant 0.14
mmpL5 779139 c.-659C>T upstream_gene_variant 0.17
mmpL5 779448 c.-968G>A upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781456 c.-104A>T upstream_gene_variant 0.13
rpsL 781664 c.105C>G synonymous_variant 0.13
rplC 801145 p.Asp113Asn missense_variant 0.14
fbiC 1303004 p.Ala25Val missense_variant 0.13
fbiC 1303495 p.Pro189Ala missense_variant 0.22
fbiC 1303691 p.Pro254Leu missense_variant 0.22
Rv1258c 1406640 p.Thr234Ile missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472731 n.886C>T non_coding_transcript_exon_variant 0.29
rrl 1473675 n.18C>A non_coding_transcript_exon_variant 0.13
rrl 1473802 n.145C>T non_coding_transcript_exon_variant 1.0
rrl 1476119 n.2462G>T non_coding_transcript_exon_variant 0.15
rrl 1476207 n.2550T>A non_coding_transcript_exon_variant 0.12
rpsA 1833922 p.Lys127Asn missense_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102691 p.Ala118Thr missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156065 p.Ala16Asp missense_variant 0.14
PPE35 2167804 p.Gly937Ser missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169194 c.1419C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.26
PPE35 2170097 c.516G>A synonymous_variant 0.15
PPE35 2170329 p.Ala95Val missense_variant 0.13
PPE35 2170368 p.Gln82Pro missense_variant 0.12
PPE35 2170392 p.Gly74Ala missense_variant 0.24
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518021 c.-94A>T upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518535 p.Ala141Thr missense_variant 1.0
eis 2714267 c.1066C>T synonymous_variant 0.2
eis 2714667 c.666G>A synonymous_variant 0.4
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747028 p.Val191Ile missense_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065711 p.Gly161Ser missense_variant 0.2
Rv2752c 3066163 p.Pro10Leu missense_variant 0.33
thyA 3073788 c.684G>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086872 p.Ile18Ser missense_variant 0.15
fbiD 3339746 p.Ala210Val missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449812 p.Asp437Asn missense_variant 0.2
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 3568590 c.90C>T synonymous_variant 0.33
Rv3236c 3612351 p.Ala256Thr missense_variant 0.33
fbiA 3640371 c.-172G>T upstream_gene_variant 1.0
fbiA 3640633 p.Asn31Asp missense_variant 0.12
alr 3841078 p.Pro115Thr missense_variant 0.13
alr 3841365 p.Gly19Asp missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.28
rpoA 3878389 p.Arg40His missense_variant 0.13
clpC1 4038963 p.Asp581Gly missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.29
clpC1 4039654 p.Thr351Ser missense_variant 0.29
clpC1 4039920 p.Arg262His missense_variant 0.4
clpC1 4040144 c.561G>C synonymous_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040841 c.-138delG upstream_gene_variant 0.17
panD 4044310 c.-29G>A upstream_gene_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241512 p.Met550Ile missense_variant 0.22
embC 4242104 p.Thr748Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.85
embA 4245333 p.Glu701Lys missense_variant 0.22
embA 4245382 p.Thr717Asn missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247516 p.Asn335Asp missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248937 c.2424G>A synonymous_variant 0.5
embB 4249158 p.Lys882Arg missense_variant 0.2
embB 4249382 p.Pro957Ser missense_variant 0.29
aftB 4267387 p.His484Tyr missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269694 p.Asp47Val missense_variant 0.22
ubiA 4269721 p.Ala38Val missense_variant 0.22
ethA 4327836 c.-363G>A upstream_gene_variant 1.0
ethR 4328143 p.Val199Met missense_variant 0.15
whiB6 4338299 p.Leu75Met missense_variant 0.25
whiB6 4338441 p.Tyr27* stop_gained 1.0
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