TB-Profiler result

Run: ERR4816192
Summary

Run ID: ERR4816192

Sample name:

Date: 01-04-2023 14:17:29

Number of reads: 581950

Percentage reads mapped: 98.52

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 5852 p.Thr205Ala missense_variant 0.25
gyrB 6007 c.768C>A synonymous_variant 0.14
gyrB 6645 p.Ser469Asn missense_variant 0.22
gyrA 7269 c.-32_-30delCAA upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7379 c.78C>T synonymous_variant 0.29
gyrA 7763 c.462T>C synonymous_variant 0.14
gyrA 7799 c.498A>G synonymous_variant 0.15
gyrA 8370 c.1069C>A synonymous_variant 0.12
gyrA 8993 p.His564Gln missense_variant 0.18
gyrA 9024 c.1723C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
gyrA 9777 p.Asn826Asp missense_variant 1.0
fgd1 490847 p.Glu22Val missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575520 p.Ala58Val missense_variant 0.67
mshA 576751 p.Lys468Asn missense_variant 0.25
ccsA 620100 c.210G>T synonymous_variant 0.12
ccsA 620148 c.258G>T synonymous_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760687 p.Phe294Tyr missense_variant 0.2
rpoB 760888 p.Thr361Asn missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762636 p.Lys944Glu missense_variant 1.0
rpoB 762834 p.Gly1010Cys missense_variant 0.5
rpoB 762879 p.Met1025Leu missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763070 c.-300T>C upstream_gene_variant 0.18
rpoB 763075 p.Thr1090Ile missense_variant 0.18
rpoB 763077 p.Val1091His missense_variant 0.18
rpoC 763088 c.-282C>G upstream_gene_variant 0.13
rpoC 763094 c.-276G>C upstream_gene_variant 0.15
rpoC 763103 c.-267G>C upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.22
rpoC 763136 c.-234C>T upstream_gene_variant 0.18
rpoB 763137 p.Ile1111Val missense_variant 0.18
rpoC 763148 c.-222G>C upstream_gene_variant 0.13
rpoC 763445 c.78_79delCG frameshift_variant 0.33
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 764404 c.1035C>T synonymous_variant 0.14
rpoC 764751 p.Val461Ala missense_variant 0.4
rpoC 764773 p.Asn468Lys missense_variant 0.4
rpoC 765023 p.Gln552* stop_gained 0.14
rpoC 765258 p.Arg630Leu missense_variant 0.21
mmpL5 775616 c.2865G>A synonymous_variant 0.15
mmpL5 775629 p.Pro951Leu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 777995 c.-995G>T upstream_gene_variant 0.14
mmpL5 778185 p.Arg99Gln missense_variant 0.29
mmpR5 778283 c.-707G>T upstream_gene_variant 0.2
mmpL5 778564 c.-84C>T upstream_gene_variant 0.17
mmpS5 778739 p.Val56Ala missense_variant 0.14
mmpR5 779308 p.Arg107Cys missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303413 p.Trp161* stop_gained 0.17
fbiC 1304094 p.Met388Ile missense_variant 0.2
fbiC 1305267 c.2337C>A synonymous_variant 0.18
embR 1416887 p.Arg154His missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrl 1474482 n.825G>T non_coding_transcript_exon_variant 1.0
rrl 1474487 n.830G>T non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 1.0
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.5
rrl 1475391 n.1734T>C non_coding_transcript_exon_variant 0.5
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
fabG1 1673987 c.551delG frameshift_variant 0.14
rpsA 1834136 p.Arg199Ser missense_variant 0.17
rpsA 1834705 c.1164C>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102772 p.His91Tyr missense_variant 0.2
katG 2154069 c.2043G>A synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155697 p.Ala139Thr missense_variant 0.17
PPE35 2167696 p.Ile973Val missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169642 p.Ala324Glu missense_variant 0.25
PPE35 2169885 p.Gly243Val missense_variant 0.29
PPE35 2170147 p.Ser156Ala missense_variant 0.5
PPE35 2170371 p.Thr81Val missense_variant 0.33
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2221965 p.Gln400His missense_variant 0.14
Rv1979c 2222882 p.Gly95Cys missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290039 c.-798C>T upstream_gene_variant 0.22
kasA 2517932 c.-182delT upstream_gene_variant 0.2
kasA 2518089 c.-26C>A upstream_gene_variant 0.13
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726266 p.Lys25Arg missense_variant 0.2
ahpC 2726752 p.Ala187Val missense_variant 0.18
folC 2746206 p.Gly465Arg missense_variant 0.17
folC 2746318 c.1281C>T synonymous_variant 0.4
folC 2746379 p.Gly407Glu missense_variant 0.4
folC 2747125 p.Met158Ile missense_variant 0.2
folC 2747167 p.Lys144Asn missense_variant 0.12
pepQ 2859359 p.Thr354Ala missense_variant 1.0
ribD 2987136 p.Val100Phe missense_variant 0.12
ribD 2987161 p.Ala108Asp missense_variant 0.12
ribD 2987601 p.Tyr255His missense_variant 0.13
Rv2752c 3065092 p.Gln367Pro missense_variant 0.12
Rv2752c 3065627 p.Ser189Thr missense_variant 0.13
Rv2752c 3067086 c.-896delG upstream_gene_variant 0.25
thyA 3074089 p.Ile128Asn missense_variant 0.12
thyA 3074287 p.Phe62Ser missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087432 p.Arg205Trp missense_variant 0.14
ald 3087456 p.Gly213Ser missense_variant 0.17
ald 3087742 p.Thr308Lys missense_variant 0.33
fbiD 3339742 c.625C>A synonymous_variant 0.5
Rv3083 3448328 c.-176G>A upstream_gene_variant 0.2
Rv3083 3448635 c.132C>T synonymous_variant 0.18
Rv3083 3449134 p.Gln211* stop_gained 0.67
Rv3083 3449776 p.Asp425Asn missense_variant 0.14
Rv3083 3449871 c.1368C>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Cys missense_variant 0.15
fprA 3475350 c.1344C>A synonymous_variant 0.14
fbiA 3640891 p.Gln117Lys missense_variant 0.12
fbiB 3642018 p.Asp162Asn missense_variant 0.5
alr 3841442 c.-22G>A upstream_gene_variant 0.12
alr 3841539 c.-119C>T upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.13
rpoA 3877664 p.Asp282Asn missense_variant 0.14
ddn 3987248 p.Asp135Glu missense_variant 0.15
clpC1 4038348 p.Ser786* stop_gained 0.12
clpC1 4039645 p.His354Asp missense_variant 0.1
clpC1 4040180 c.525C>A synonymous_variant 0.25
embC 4239780 c.-83G>T upstream_gene_variant 0.12
embC 4240475 p.Ala205Ser missense_variant 0.18
embC 4240480 c.618G>A synonymous_variant 0.18
embC 4240489 c.627A>G synonymous_variant 0.18
embC 4240495 c.633T>C synonymous_variant 0.17
embC 4240512 p.Ser217Thr missense_variant 0.17
embC 4240514 p.Val218Ile missense_variant 0.17
embC 4240519 c.657T>C synonymous_variant 0.17
embC 4240543 c.681G>C synonymous_variant 0.11
embC 4240769 p.Val303Met missense_variant 0.25
embC 4241245 c.1383C>T synonymous_variant 0.11
embC 4241928 p.Arg689Pro missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242255 p.Pro798Leu missense_variant 0.22
embC 4242264 p.Glu801Val missense_variant 0.13
embC 4242449 p.Met863Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242950 p.Gly1030Arg missense_variant 0.13
embA 4243710 p.Gly160Trp missense_variant 0.18
embA 4244065 p.Leu278Gln missense_variant 0.25
embA 4244214 p.Ala328Thr missense_variant 0.2
embA 4245340 p.Gly703Asp missense_variant 0.18
embA 4245387 c.2157delC frameshift_variant 0.15
embB 4246587 p.Gly25Glu missense_variant 0.25
embB 4247097 p.Pro195His missense_variant 0.17
embB 4247772 p.Glu420Gly missense_variant 0.33
aftB 4267003 c.1834C>A synonymous_variant 0.22
aftB 4267130 c.1707C>T synonymous_variant 0.14
aftB 4267338 p.Leu500His missense_variant 0.2
aftB 4268741 c.96G>A synonymous_variant 0.17
ubiA 4269837 c.-4T>G upstream_gene_variant 0.33
ethA 4326078 p.Arg466Trp missense_variant 0.17
ethA 4326155 p.Leu440Pro missense_variant 0.14
ethA 4327424 p.Val17Asp missense_variant 0.4
ethR 4327928 p.Ala127Asp missense_variant 0.22
ethA 4328270 c.-797C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408470 c.-268G>A upstream_gene_variant 0.18