TB-Profiler result

Run: ERR028330
Summary

Run ID: ERR028330

Sample name:

Date: 31-03-2023 08:22:15

Number of reads: 738958

Percentage reads mapped: 98.86

Strain: lineage4.6.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.2
lineage4.6 Euro-American T;LAM None 0.09
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.07
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.13
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.06
lineage1.2.2.2 Indo-Oceanic NA RD239 0.05
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 6112 p.Met291Ile missense_variant 0.48
gyrB 6124 c.885C>T synonymous_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.26
gyrA 8019 p.Thr240Ala missense_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.72
ccsA 620463 c.573C>A synonymous_variant 0.24
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 0.38
rpoC 762434 c.-936T>G upstream_gene_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 0.85
rpoC 763552 c.183C>T synonymous_variant 0.16
rpoC 763884 p.Ala172Val missense_variant 0.43
rpoC 763886 c.517C>A synonymous_variant 0.43
rpoC 765171 p.Pro601Leu missense_variant 0.44
rpoC 766582 c.3213C>A synonymous_variant 0.21
rpoC 767314 p.Tyr1315* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.69
mmpL5 777451 p.Val344Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.13
embR 1416410 p.Leu313Arg missense_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 0.67
embR 1417501 c.-154A>C upstream_gene_variant 0.22
atpE 1461019 c.-26C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473414 n.-244G>C upstream_gene_variant 0.1
rrl 1474619 n.962G>T non_coding_transcript_exon_variant 0.11
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.19
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.17
inhA 1674465 c.264C>T synonymous_variant 0.12
inhA 1674892 p.Asn231Asp missense_variant 0.19
rpsA 1834159 c.618G>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.38
katG 2154724 p.Arg463Leu missense_variant 0.64
katG 2156543 c.-432G>A upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.96
PPE35 2167983 p.Gly877Asp missense_variant 0.54
PPE35 2168604 p.Pro670Leu missense_variant 0.12
PPE35 2168742 p.Gly624Asp missense_variant 0.2
PPE35 2169121 p.Val498Met missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36
Rv1979c 2222732 c.432delT frameshift_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.23
pncA 2289365 c.-125delC upstream_gene_variant 0.45
kasA 2518132 c.18C>T synonymous_variant 0.42
eis 2714366 p.Val323Leu missense_variant 0.21
ahpC 2726051 c.-142G>A upstream_gene_variant 0.59
ahpC 2726105 c.-88G>A upstream_gene_variant 0.56
Rv2752c 3064632 c.1560C>T synonymous_variant 0.48
Rv2752c 3064741 p.Gly484Ala missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 0.81
Rv3083 3448714 p.Asp71His missense_variant 0.44
Rv3083 3449262 c.759G>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.47
fprA 3475159 p.Asn385Asp missense_variant 0.47
fprA 3475280 p.Val425Gly missense_variant 0.4
whiB7 3568507 p.Gln58Arg missense_variant 0.33
fbiB 3641955 p.Gly141Arg missense_variant 0.29
ddn 3986745 c.-99A>C upstream_gene_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4040517 p.Val63Ala missense_variant 0.5
panD 4044402 c.-121T>C upstream_gene_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.55
embC 4241042 p.Asn394Asp missense_variant 0.78
embC 4241429 p.Phe523Val missense_variant 0.31
embC 4242075 p.Arg738Gln missense_variant 0.31
embA 4242475 c.-758G>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243709 c.477C>T synonymous_variant 0.17
embA 4243848 p.Val206Met missense_variant 0.43
embA 4244096 c.864C>T synonymous_variant 0.25
embA 4244272 p.Leu347Arg missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 0.36
embA 4246225 p.Gly998Val missense_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.6
embB 4248725 p.Ser738Ala missense_variant 0.21
embB 4249195 c.2682C>A synonymous_variant 0.23
aftB 4267960 p.Val293Met missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 0.35
aftB 4269606 c.-770T>C upstream_gene_variant 0.47
ethA 4327672 c.-199G>A upstream_gene_variant 0.2
whiB6 4338203 p.Arg107Cys missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.52
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407848 p.Ala119Thr missense_variant 0.2
gid 4407873 c.330G>T synonymous_variant 0.25