TB-Profiler result

Run: ERR4872093
Summary

Run ID: ERR4872093

Sample name:

Date: 01-04-2023 21:21:38

Number of reads: 4642657

Percentage reads mapped: 89.69

Strain: lineage5.2

Drug-resistance: MDR-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 0.98
lineage5.2 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 761100 p.Gln432Lys missense_variant 0.93 rifampicin
rpoB 761139 p.His445Asp missense_variant 0.93 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embA 4243203 c.-29_-28delCT upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol
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 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
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 576108 p.Ala254Gly missense_variant 0.21
rpoB 760841 c.1035T>C synonymous_variant 0.13
rpoB 760845 p.Thr347Ala missense_variant 0.14
rpoB 760859 c.1053T>C synonymous_variant 0.14
rpoB 760862 c.1056G>C synonymous_variant 0.14
rpoB 760925 c.1119T>C synonymous_variant 0.15
rpoB 760928 c.1122G>C synonymous_variant 0.16
rpoB 760934 c.1128C>T synonymous_variant 0.16
rpoB 760946 c.1140A>G synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.14
rpoB 760985 c.1179G>C synonymous_variant 0.14
rpoB 762131 c.2325C>G synonymous_variant 0.15
rpoB 762140 c.2334G>C synonymous_variant 0.14
rpoB 762143 c.2337T>C synonymous_variant 0.14
rpoB 762149 c.2343G>C synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763702 c.333C>G synonymous_variant 0.13
rpoC 763774 c.405G>C synonymous_variant 0.14
rpoC 763792 p.Glu141Asp missense_variant 0.14
rpoC 766864 c.3495G>C synonymous_variant 0.13
rpoC 766894 c.3525T>C synonymous_variant 0.15
rpoC 766900 c.3531T>C synonymous_variant 0.15
rpoC 766933 c.3564A>G synonymous_variant 0.16
rpoC 766945 c.3576A>G synonymous_variant 0.14
rpoC 767011 c.3642G>C synonymous_variant 0.13
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
rpsL 781715 c.156T>C synonymous_variant 0.15
rpsL 781728 c.169T>C synonymous_variant 0.15
rpsL 781736 c.177T>C synonymous_variant 0.14
rpsL 781742 c.183C>T synonymous_variant 0.14
rpsL 781748 c.189C>G synonymous_variant 0.16
rpsL 781754 c.195G>T synonymous_variant 0.16
rpsL 781760 c.201T>C synonymous_variant 0.17
rpsL 781772 c.213C>T synonymous_variant 0.15
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303761 c.831T>C synonymous_variant 0.14
fbiC 1303785 c.855G>C synonymous_variant 0.14
fbiC 1303789 p.Ile287Val missense_variant 0.14
fbiC 1303797 c.867A>G synonymous_variant 0.16
fbiC 1303818 c.888C>G synonymous_variant 0.16
fbiC 1303827 c.897A>G synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.13
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.14
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.18
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.19
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.21
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.22
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.23
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.22
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.22
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.22
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.22
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.12
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.15
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.13
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
rpsA 1834609 c.1068T>C synonymous_variant 0.14
rpsA 1834633 c.1092A>G synonymous_variant 0.15
rpsA 1834639 c.1098T>C synonymous_variant 0.15
rpsA 1834654 p.Glu371Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.97
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
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 0.97
kasA 2518132 c.18C>T synonymous_variant 1.0
Rv2752c 3064664 p.Lys510Gln missense_variant 0.98
thyX 3067949 c.-4C>T upstream_gene_variant 0.99
thyA 3073920 c.552C>G synonymous_variant 0.14
thyA 3073977 c.495A>G synonymous_variant 0.14
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087172 p.Glu118Ala missense_variant 0.99
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612237 p.Ala294Ser missense_variant 0.99
alr 3840932 c.489C>T synonymous_variant 0.98
rpoA 3877679 p.Ala277Ser missense_variant 0.14
rpoA 3877692 c.816G>C synonymous_variant 0.14
rpoA 3877743 c.765T>C synonymous_variant 0.16
rpoA 3877764 c.744C>G synonymous_variant 0.14
rpoA 3877770 c.738A>G synonymous_variant 0.14
rpoA 3877782 c.726T>C synonymous_variant 0.13
rpoA 3877791 c.717C>G synonymous_variant 0.14
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4038755 c.1950G>C synonymous_variant 0.14
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 0.98
embA 4245147 p.Pro639Ser missense_variant 0.92
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249495 c.2982C>T synonymous_variant 0.94
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326914 p.Ala187Glu missense_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
ethR 4328190 p.Glu214Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407946 p.Leu86Pro missense_variant 1.0