TB-Profiler result

Run: ERR2229325
Summary

Run ID: ERR2229325

Sample name:

Date: 31-03-2023 17:02:37

Number of reads: 1393852

Percentage reads mapped: 98.05

Strain: lineage4.8

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.28 kanamycin, capreomycin, aminoglycosides, amikacin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7945 p.Thr215Asn missense_variant 0.12
fgd1 491133 c.351A>T synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.41
ccsA 620842 p.His318Asn missense_variant 0.14
rpoB 760762 p.Gly319Val missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.23
rpoC 764943 p.His525Pro missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.24
mmpL5 777164 c.1317C>T synonymous_variant 0.27
mmpL5 777920 c.561C>A synonymous_variant 0.18
mmpL5 777948 p.Pro178Gln missense_variant 0.25
mmpS5 778851 p.Ala19Pro missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305024 c.2094C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.19
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.21
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.22
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.13
rrl 1474495 n.838G>T non_coding_transcript_exon_variant 0.13
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.14
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.13
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.11
rrl 1474508 n.851C>G non_coding_transcript_exon_variant 0.11
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.13
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.13
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.17
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.19
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.13
rrl 1475137 n.1480A>G non_coding_transcript_exon_variant 0.11
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.18
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.14
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
inhA 1674691 p.Ala164Ser missense_variant 0.13
inhA 1674861 p.Glu220Asp missense_variant 0.12
rpsA 1834747 p.Glu402Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918645 p.Asn236Asp missense_variant 0.2
ndh 2102116 c.927G>T synonymous_variant 0.18
katG 2154212 p.Leu634Ile missense_variant 0.15
katG 2154222 c.1890C>G synonymous_variant 0.23
katG 2155172 p.Thr314Ser missense_variant 0.12
katG 2155508 p.Ala202Ser missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.13
PPE35 2169491 c.1122T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.73
PPE35 2170053 p.Thr187Ser missense_variant 0.71
Rv1979c 2222337 c.828G>T synonymous_variant 0.18
Rv1979c 2222806 p.Val120Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289551 c.-310C>A upstream_gene_variant 0.21
eis 2715076 p.Ala86Val missense_variant 0.12
folC 2746938 p.Thr221Ser missense_variant 0.12
folC 2746943 p.Ile219Ser missense_variant 0.12
ribD 2987034 p.Gly66Ser missense_variant 0.14
Rv2752c 3065744 c.447delC frameshift_variant 0.15
Rv2752c 3066234 c.-43G>T upstream_gene_variant 0.14
thyA 3074258 p.Leu72Met missense_variant 0.12
ald 3087229 p.Ala137Asp missense_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fbiA 3640494 c.-49C>T upstream_gene_variant 0.14
fbiB 3641968 p.Ala145Gly missense_variant 0.18
fbiB 3642803 c.1269C>T synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
clpC1 4039606 p.Glu367Lys missense_variant 0.13
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4039884 p.Lys274Arg missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.13
embC 4241822 p.Phe654Leu missense_variant 0.12
embC 4242038 p.Ala726Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242901 c.-332G>T upstream_gene_variant 0.15
embA 4245428 p.Ser732Arg missense_variant 0.12
embA 4246117 p.Pro962Arg missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.64
embB 4246555 c.42G>C synonymous_variant 0.69
embB 4246556 p.Ala15Pro missense_variant 0.69
embB 4246563 p.Leu17Trp missense_variant 0.55
embB 4246567 c.54G>T synonymous_variant 0.36
embB 4248837 c.2328delC frameshift_variant 0.11
embB 4249083 p.Thr857Ile missense_variant 0.13
ubiA 4269194 p.Thr214Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407658 p.Gly182Val missense_variant 0.13
gid 4407669 p.Met178Ile missense_variant 0.12
gid 4407676 p.Arg176His missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0