TB-Profiler result

Run: SRR6982013
Summary

Run ID: SRR6982013

Sample name:

Date: 04-04-2023 18:24:42

Number of reads: 339965

Percentage reads mapped: 99.66

Strain: lineage2.2.1

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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 5186 c.-54C>A upstream_gene_variant 0.12
gyrB 5872 p.Glu211Asp missense_variant 0.15
gyrB 6260 p.Lys341Glu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8181 p.Gly294Cys missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.29
fgd1 491347 p.Gly189Cys missense_variant 0.17
fgd1 491492 p.Pro237His missense_variant 0.15
fgd1 491540 p.Ser253* stop_gained 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575531 p.Thr62Ser missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619784 c.-107G>T upstream_gene_variant 0.22
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.27
rpoB 759720 c.-87C>A upstream_gene_variant 0.14
rpoB 761803 p.Met666Lys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763204 p.Ser1133* stop_gained 0.17
rpoC 763610 p.Glu81* stop_gained 0.2
rpoC 764186 p.Glu273* stop_gained 0.12
rpoC 764225 p.Gly286Trp missense_variant 0.12
rpoC 764469 p.Val367Ala missense_variant 0.12
rpoC 766500 p.Ala1044Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.94
mmpL5 776919 c.1561delA frameshift_variant 0.25
mmpL5 778431 p.Arg17Met missense_variant 0.12
mmpL5 779409 c.-929C>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800700 c.-109C>T upstream_gene_variant 0.2
fbiC 1304907 c.1977C>G synonymous_variant 0.12
fbiC 1305009 c.2079C>A synonymous_variant 0.29
fbiC 1305279 p.His783Gln missense_variant 0.22
Rv1258c 1406417 c.923delT frameshift_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406827 p.Thr172Ala missense_variant 0.2
Rv1258c 1406964 p.Ser126* stop_gained 0.2
Rv1258c 1407424 c.-84C>T upstream_gene_variant 0.13
embR 1416365 p.His328Arg missense_variant 0.14
atpE 1460922 c.-123C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472846 n.1001C>A non_coding_transcript_exon_variant 0.12
rrl 1474234 n.577G>T non_coding_transcript_exon_variant 0.18
rrl 1474573 n.916C>A non_coding_transcript_exon_variant 0.12
rrl 1476028 n.2371A>G non_coding_transcript_exon_variant 0.2
inhA 1674384 c.183C>A synonymous_variant 0.25
inhA 1674617 p.Asn139Ser missense_variant 0.11
rpsA 1833542 c.1A>G start_lost 0.13
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918415 p.Ser159Trp missense_variant 0.15
katG 2154179 p.Val645Leu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154958 p.Arg385Leu missense_variant 0.15
katG 2155146 c.966G>C synonymous_variant 0.17
katG 2155396 p.Pro239Leu missense_variant 0.2
katG 2156014 p.Gly33Asp missense_variant 0.12
katG 2156256 c.-145C>A upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169142 p.Thr491Ala missense_variant 0.25
PPE35 2169518 c.1094delG frameshift_variant 0.18
Rv1979c 2222516 p.Thr217Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288878 p.Gln122Lys missense_variant 0.13
pncA 2289969 c.-728G>T upstream_gene_variant 0.18
kasA 2519119 c.1005G>T synonymous_variant 0.4
eis 2714412 c.921G>T synonymous_variant 0.11
eis 2714526 c.805_806delAC frameshift_variant 1.0
folC 2746370 p.Arg410Gln missense_variant 0.2
ribD 2986706 c.-133C>A upstream_gene_variant 0.13
ribD 2986865 c.27C>G synonymous_variant 0.15
ribD 2987445 p.Val203Phe missense_variant 0.13
Rv2752c 3065564 p.Gly210Cys missense_variant 0.25
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
thyA 3073872 c.600C>A synonymous_variant 0.17
thyA 3074313 c.159A>G synonymous_variant 0.12
thyA 3074400 c.72C>A synonymous_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339333 c.216G>A synonymous_variant 1.0
Rv3083 3448472 c.-32A>T upstream_gene_variant 0.25
Rv3083 3448829 p.Trp109Leu missense_variant 0.14
Rv3083 3449072 p.Val190Ala missense_variant 0.15
Rv3083 3449686 p.Trp395Arg missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641358 c.-177G>T upstream_gene_variant 0.12
fbiB 3642107 p.Glu191Asp missense_variant 0.13
fbiB 3642339 p.Asp269Tyr missense_variant 0.2
fbiB 3642365 p.Glu277Asp missense_variant 0.17
fbiB 3642516 p.Ala328Ser missense_variant 0.18
fbiB 3642574 p.Val347Ala missense_variant 0.17
alr 3841103 c.318C>T synonymous_variant 0.12
rpoA 3878691 c.-184G>T upstream_gene_variant 0.67
clpC1 4038206 c.2499C>A synonymous_variant 0.29
clpC1 4038918 p.Gly596Val missense_variant 0.14
clpC1 4039968 p.Gln246Arg missense_variant 0.15
clpC1 4040854 c.-150T>C upstream_gene_variant 0.12
embC 4240921 c.1059C>A synonymous_variant 0.14
embC 4241246 p.Arg462Trp missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242777 p.Gln972Arg missense_variant 0.12
embC 4242858 p.His999Arg missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244085 p.Pro285Thr missense_variant 0.11
embA 4244448 c.1220delC frameshift_variant 0.14
embA 4245081 p.Ala617Thr missense_variant 0.13
embB 4247994 p.Phe494Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268547 p.Leu97Arg missense_variant 0.14
ethR 4326877 c.-672G>T upstream_gene_variant 0.25
ethR 4328024 p.Arg159Gln missense_variant 0.17
whiB6 4338230 p.Leu98Met missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0