TB-Profiler result

Run: ERR046918
Summary

Run ID: ERR046918

Sample name:

Date: 31-03-2023 08:57:15

Number of reads: 4926696

Percentage reads mapped: 99.18

Strain: lineage5.1.3

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
lineage5.1.3 West-Africa 1 AFRI_2;AFRI_3 RD711 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
rpoB 760314 p.Val170Phe missense_variant 0.14 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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.23
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 0.21
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.21
rrs 1471658 n.-188T>G upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18
rrl 1475370 n.1713G>A non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.16
inhA 1673338 c.-864G>A upstream_gene_variant 0.99
inhA 1674892 p.Asn231Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.3
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
PPE35 2169866 c.747G>C synonymous_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288951 c.291T>G synonymous_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518323 p.Ser70Asn missense_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.2
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.17
fbiD 3339550 p.Gly145Trp missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.26
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.17
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878493 c.15G>A synonymous_variant 0.99
rpoA 3878601 c.-94C>G upstream_gene_variant 0.19
rpoA 3878641 c.-135delG upstream_gene_variant 0.13
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987013 p.Gly57Ala missense_variant 0.18
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.23
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 0.98
embC 4241056 c.1194C>G synonymous_variant 0.21
embC 4241456 p.Ala532Pro missense_variant 0.39
embC 4242476 p.Pro872Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.35
embC 4242827 p.Leu989Val missense_variant 0.16
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248725 p.Ser738Ala missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.18
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 0.99
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0