TB-Profiler result

Run: ERR2516310
Summary

Run ID: ERR2516310

Sample name:

Date: 31-03-2023 21:26:54

Number of reads: 1501525

Percentage reads mapped: 98.57

Strain: lineage5.2

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.2 West-Africa 1 AFRI_2;AFRI_3 RD711 0.98
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 6170 p.His311Asn missense_variant 0.24
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
fgd1 491318 p.Pro179Gln missense_variant 0.22
fgd1 491321 p.Ala180Glu missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619791 c.-100G>A upstream_gene_variant 1.0
ccsA 620679 c.789C>A synonymous_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 p.Lys160Asn missense_variant 0.22
rpoC 766722 p.Pro1118Gln missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777245 c.1236G>T synonymous_variant 0.38
mmpL5 777439 p.Ala348Ser missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801333 c.525G>T synonymous_variant 0.26
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304856 c.1926C>A synonymous_variant 0.29
Rv1258c 1407198 p.Ala48Asp missense_variant 0.17
embR 1416600 p.Leu250Ile missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
inhA 1674653 p.Pro151Gln missense_variant 0.22
rpsA 1833400 c.-142G>T upstream_gene_variant 0.22
rpsA 1833427 c.-115G>T upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154545 p.Glu523* stop_gained 0.21
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156477 c.-366C>T upstream_gene_variant 0.22
PPE35 2167857 p.Trp919* stop_gained 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289638 c.-397C>A upstream_gene_variant 0.31
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518595 p.Arg161Ser missense_variant 0.38
kasA 2518652 p.His180Asn missense_variant 0.4
folC 2746153 p.Phe482Leu missense_variant 0.33
pepQ 2859938 p.Gly161Cys missense_variant 0.25
Rv2752c 3065951 p.His81Asn missense_variant 0.23
thyX 3067276 p.Pro224Thr missense_variant 0.2
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3448586 p.Pro28His missense_variant 0.27
Rv3083 3448635 c.132C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474646 p.Glu214* stop_gained 0.38
fprA 3474921 p.Lys305Asn missense_variant 0.31
fprA 3474979 p.Arg325Ser missense_variant 0.25
fprA 3475144 p.Asp380Tyr missense_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611986 c.1131G>T synonymous_variant 0.2
Rv3236c 3612167 p.Gly317Val missense_variant 0.24
Rv3236c 3612783 p.Gly112Trp missense_variant 0.36
Rv3236c 3612796 c.321G>T synonymous_variant 0.27
Rv3236c 3612803 p.Ala105Val missense_variant 0.2
fbiB 3642257 p.Phe241Leu missense_variant 0.12
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878560 c.-53C>A upstream_gene_variant 0.4
rpoA 3878592 c.-85C>A upstream_gene_variant 0.67
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
panD 4044114 c.168C>A synonymous_variant 0.31
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242035 p.Gln725Lys missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243033 p.Trp1057Cys missense_variant 0.2
embA 4243237 p.Pro2His missense_variant 0.37
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244505 p.Gly425Trp missense_variant 0.21
embA 4244635 p.Val468Ala missense_variant 0.92
embA 4244874 p.Pro548Thr missense_variant 0.2
embA 4244916 p.Leu562Met missense_variant 0.17
embA 4245147 p.Pro639Ser missense_variant 1.0
embB 4245533 c.-981C>A upstream_gene_variant 0.27
embA 4245606 p.Leu792Met missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249596 p.Trp1028Leu missense_variant 0.24
embB 4249714 p.Phe1067Leu missense_variant 0.28
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269942 c.-109C>A upstream_gene_variant 0.24
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0