TB-Profiler result

Run: ERR233362
Summary

Run ID: ERR233362

Sample name:

Date: 13-08-2022 03:00:23

Number of reads: 7942543

Percentage reads mapped: 97.92

Strain: lineage6.1.1

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
lineage6 West-Africa 2 AFRI_1 RD702 0.99
lineage6.1.1 West-Africa 2 AFRI_1 RD702 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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.25
gyrA 8493 p.Leu398Phe missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491668 p.Lys296Glu missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.2
mshA 576751 p.Lys468Asn missense_variant 0.17
rpoB 760855 p.Thr350Ile missense_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761723 p.Glu639Asp missense_variant 0.98
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.18
rpoC 764751 p.Val461Gly missense_variant 0.22
rpoC 764905 p.Phe512Leu missense_variant 0.16
rpoC 766231 c.2862T>C synonymous_variant 0.98
rpoC 767305 p.Tyr1312* stop_gained 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.2
Rv1258c 1406685 p.Val219Ala missense_variant 1.0
Rv1258c 1406750 c.591C>A synonymous_variant 0.19
embR 1416633 p.Leu239Val missense_variant 1.0
embR 1417233 c.115C>T synonymous_variant 0.16
atpE 1461251 c.207G>T synonymous_variant 1.0
rrs 1471658 n.-188T>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.2
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.24
fabG1 1673449 p.Thr4Pro missense_variant 0.21
fabG1 1673546 p.Ala36Gly missense_variant 0.27
inhA 1674434 p.Val78Ala missense_variant 1.0
inhA 1674892 p.Asn231Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.45
ndh 2102891 p.Phe51Ser missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.2
PPE35 2169999 p.Ala205Val missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289706 c.-465C>A upstream_gene_variant 0.99
pncA 2290023 c.-782A>C upstream_gene_variant 0.35
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2725954 c.-239C>T upstream_gene_variant 0.17
ahpC 2726737 p.Asp182Ala missense_variant 0.14
ahpC 2726756 c.564C>G synonymous_variant 0.18
folC 2746186 c.1413G>C synonymous_variant 0.15
Rv2752c 3064552 p.Arg547Pro missense_variant 0.11
Rv2752c 3064741 p.Gly484Ala missense_variant 0.21
Rv2752c 3065265 c.927C>G synonymous_variant 0.2
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087811 p.Ala331Gly missense_variant 0.14
Rv3083 3449058 p.Ser185Arg missense_variant 0.27
Rv3083 3449673 p.Tyr390* stop_gained 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.24
Rv3236c 3612143 p.Arg325His missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.18
rpoA 3878641 c.-135delG upstream_gene_variant 0.25
ddn 3987013 p.Gly57Ala missense_variant 0.28
clpC1 4039363 p.Ala448Pro missense_variant 0.16
clpC1 4039680 p.Phe342Ser missense_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4239973 c.111T>G synonymous_variant 0.14
embC 4240355 p.Ala165Pro missense_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.16
embC 4241456 p.Ala532Pro missense_variant 0.24
embC 4241783 p.Trp641Gly missense_variant 0.23
embC 4241843 p.Leu661Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
embA 4243570 p.Thr113Arg missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248725 p.Ser738Ala missense_variant 0.15
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.99
aftB 4269522 c.-686C>T upstream_gene_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408034 p.Glu57Lys missense_variant 1.0
gid 4408329 c.-127C>G upstream_gene_variant 0.21