TB-Profiler result

Run: ERR4832054
Summary

Run ID: ERR4832054

Sample name:

Date: 01-04-2023 21:17:38

Number of reads: 693534

Percentage reads mapped: 98.43

Strain: lineage2.2.1.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.96
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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776464 p.Ser673Thr missense_variant 0.18
mmpL5 776473 p.Gln670Lys missense_variant 0.17
mmpL5 777163 p.Gln440Lys missense_variant 0.11
mmpL5 778101 p.Gln127Pro missense_variant 0.11
mmpL5 779010 c.-530G>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800764 c.-45C>A upstream_gene_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472099 n.254G>A non_coding_transcript_exon_variant 0.13
rrs 1472404 n.559G>T non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473280 n.1435G>C non_coding_transcript_exon_variant 0.11
rrl 1474134 n.477G>T non_coding_transcript_exon_variant 0.12
rrl 1474408 n.751G>T non_coding_transcript_exon_variant 0.18
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.25
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.24
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.24
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.24
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.11
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.11
rrl 1475062 n.1405A>T non_coding_transcript_exon_variant 0.17
rrl 1475953 n.2296A>G non_coding_transcript_exon_variant 0.17
fabG1 1673507 p.Gly23Glu missense_variant 0.15
inhA 1673660 c.-542C>A upstream_gene_variant 0.12
rpsA 1833558 p.Val6Ala missense_variant 0.18
rpsA 1833676 c.135A>G synonymous_variant 0.12
rpsA 1833790 c.249T>C synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154456 c.1656A>T synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155523 p.Tyr197Asn missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168804 p.Gly603Arg missense_variant 0.13
PPE35 2169432 p.Pro394Gln missense_variant 0.13
Rv1979c 2222090 c.1075T>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288857 p.Asp129Tyr missense_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
thyA 3073952 p.Val174Leu missense_variant 0.25
ald 3086782 c.-38T>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448902 c.399C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568427 p.Arg85Ser missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878154 c.354G>T synonymous_variant 0.15
ddn 3986939 c.96C>T synonymous_variant 0.12
clpC1 4039068 p.Ser546* stop_gained 0.14
clpC1 4040550 p.Leu52Ser missense_variant 0.11
embC 4241432 p.Met524Val missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.98
embA 4245169 p.Val646Gly missense_variant 0.11
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248339 p.Leu609Pro missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267922 c.915G>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0