TB-Profiler result

Run: ERR11050123
Summary

Run ID: ERR11050123

Sample name:

Date: 02-04-2023 12:31:09

Number of reads: 436125

Percentage reads mapped: 99.21

Strain: lineage5.3

Drug-resistance: RR-TB

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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
lineage5.3 West-Africa 1 AFRI_2;AFRI_3 RD711 0.99
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
rpoB 761083 p.Gly426Asp missense_variant 0.2 rifampicin
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 5658 p.Lys140Thr missense_variant 0.22
gyrB 5972 p.Lys245Glu missense_variant 0.12
gyrB 6365 p.Gly376Ser missense_variant 0.13
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 490884 c.102C>T synonymous_variant 0.17
fgd1 491315 p.Gly178Ala missense_variant 0.38
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619945 p.Thr19Ser missense_variant 0.4
rpoB 760181 c.377delC frameshift_variant 0.12
rpoB 761482 p.Ala559Gly missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764348 p.Met327Leu missense_variant 0.17
rpoC 764367 p.Gly333Ala missense_variant 0.2
rpoC 764534 p.Arg389Gly missense_variant 0.43
rpoC 767099 p.Lys1244Glu missense_variant 0.18
mmpL5 775624 p.Pro953Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775751 c.2730C>A synonymous_variant 1.0
mmpL5 775902 p.Glu860Gly missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776223 p.Gly753Glu missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800793 c.-16G>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303157 p.His76Pro missense_variant 0.25
fbiC 1304646 c.1716T>G synonymous_variant 0.24
fbiC 1305485 p.Ala852Asp missense_variant 1.0
embR 1416232 p.Cys372Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476394 n.2737C>G non_coding_transcript_exon_variant 0.2
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.22
fabG1 1673561 p.Lys41Met missense_variant 0.25
inhA 1674422 p.Leu74Trp missense_variant 0.25
inhA 1674556 p.Gly119Arg missense_variant 0.17
rpsA 1834651 c.1110C>T synonymous_variant 0.14
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 2154724 p.Arg463Leu missense_variant 1.0
katG 2156549 c.-438A>C upstream_gene_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518247 p.Ala45Pro missense_variant 0.14
kasA 2518520 p.Lys136Glu missense_variant 0.2
kasA 2518939 c.825T>C synonymous_variant 0.14
eis 2714764 p.Leu190Gln missense_variant 0.33
ahpC 2726741 c.549G>T synonymous_variant 0.2
pepQ 2859342 c.1077G>A synonymous_variant 0.2
Rv2752c 3064823 p.Val457Leu missense_variant 0.33
thyX 3067942 p.Ala2Pro missense_variant 0.6
thyA 3074064 c.408C>T synonymous_variant 0.33
thyA 3074584 c.-113G>A upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
ald 3087763 p.Asn315Thr missense_variant 0.29
fprA 3473958 c.-49C>A upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474050 p.Ala15Gly missense_variant 0.75
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568749 c.-71delC upstream_gene_variant 0.29
Rv3236c 3612909 p.Leu70Val missense_variant 0.33
fbiA 3640394 c.-149G>A upstream_gene_variant 1.0
fbiB 3642384 p.Leu284Phe missense_variant 0.33
alr 3840932 c.489C>T synonymous_variant 1.0
ddn 3986852 c.9A>G synonymous_variant 0.11
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4038921 p.Phe595Tyr missense_variant 0.25
clpC1 4040550 p.Leu52Trp missense_variant 0.2
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
panD 4044134 p.Asp50Asn missense_variant 0.12
panD 4044303 c.-22T>C upstream_gene_variant 0.17
embC 4239739 c.-124A>T upstream_gene_variant 0.22
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240760 p.Met300Leu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243012 p.Lys1050Asn missense_variant 0.25
embA 4243272 p.Arg14Cys missense_variant 0.2
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embA 4246287 p.Asn1019His missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267134 p.Cys568Ser missense_variant 0.2
aftB 4267900 p.Ala313Ser missense_variant 0.33
aftB 4267978 p.Pro287Thr missense_variant 0.4
aftB 4268623 p.Trp72Gly missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269666 c.-830G>A upstream_gene_variant 0.13
ubiA 4269727 p.Pro36Arg missense_variant 0.22
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