TB-Profiler result

Run: ERR2704691
Summary

Run ID: ERR2704691

Sample name:

Date: 31-03-2023 23:03:41

Number of reads: 581325

Percentage reads mapped: 99.02

Strain: lineage5.1.4

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.1.4 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
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 5509 c.270C>A synonymous_variant 0.15
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7424 c.123G>T synonymous_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8262 p.Asp321Tyr missense_variant 0.15
gyrA 8353 p.Gly351Val missense_variant 0.22
gyrA 8800 p.Ala500Val missense_variant 0.17
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 491742 c.960T>C synonymous_variant 1.0
rpoB 761591 p.Asp595Glu missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763946 p.Ala193Thr missense_variant 0.17
rpoC 766333 c.2964G>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775753 c.2727delC frameshift_variant 1.0
mmpL5 775827 p.Gly885Glu missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776522 c.1959G>A synonymous_variant 0.22
mmpS5 778619 p.Ala96Glu missense_variant 0.33
mmpS5 778808 p.Gly33Val missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801114 c.306C>A synonymous_variant 0.2
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303283 p.Gly118Val missense_variant 0.25
fbiC 1304763 c.1833C>A synonymous_variant 0.29
Rv1258c 1406543 c.798G>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473617 n.-41T>A upstream_gene_variant 0.5
rrl 1476362 n.2705C>A non_coding_transcript_exon_variant 0.67
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
inhA 1673769 c.-433C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2102350 c.693G>T synonymous_variant 0.17
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
ndh 2103180 c.-138C>T upstream_gene_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155594 p.Leu173Pro missense_variant 0.12
katG 2155684 p.Lys143Met missense_variant 0.15
katG 2155903 p.Thr70Asn missense_variant 0.22
PPE35 2167697 c.2915delA frameshift_variant 0.25
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 2517920 c.-195G>T upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
thyA 3073695 c.777T>C synonymous_variant 0.18
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087142 p.Leu108Ser missense_variant 0.15
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
ald 3087635 c.816C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642670 p.Ala379Glu missense_variant 0.25
alr 3840932 c.489C>T synonymous_variant 1.0
alr 3841495 c.-75G>A upstream_gene_variant 0.33
rpoA 3878374 p.Ser45Leu missense_variant 0.29
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4038520 p.Arg729Trp missense_variant 0.25
clpC1 4038791 c.1914G>T synonymous_variant 0.4
clpC1 4040541 p.Ser55* stop_gained 0.22
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 1.0
embC 4241428 c.1566G>A synonymous_variant 0.33
embC 4241710 c.1848G>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243647 p.Leu139Met missense_variant 0.18
embA 4243674 p.Ala148Ser missense_variant 0.15
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
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
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 1.0
whiB6 4338546 c.-25G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408241 c.-39G>T upstream_gene_variant 0.18