TB-Profiler result

Run: ERR3170466
Summary

Run ID: ERR3170466

Sample name:

Date: 01-04-2023 00:46:38

Number of reads: 962960

Percentage reads mapped: 99.45

Strain: lineage5.1.2

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 0.99
lineage5.1.2 West-Africa 1 AFRI_2;AFRI_3 RD711 0.99
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 5996 p.Tyr253Asn missense_variant 0.21
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6473 p.Ser412Pro missense_variant 0.14
gyrB 6518 p.Val427Leu missense_variant 0.2
gyrB 6546 p.Gly436Asp missense_variant 0.25
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 1.0
fgd1 491374 p.Lys198* stop_gained 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.92
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472882 n.1037A>T non_coding_transcript_exon_variant 0.18
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>T non_coding_transcript_exon_variant 0.15
rrl 1473994 n.337C>T non_coding_transcript_exon_variant 0.2
rrl 1474033 n.376A>T non_coding_transcript_exon_variant 0.29
rrl 1475096 n.1439A>T non_coding_transcript_exon_variant 0.4
rrl 1475621 n.1964T>A non_coding_transcript_exon_variant 0.3
rrl 1475886 n.2229T>A non_coding_transcript_exon_variant 0.43
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
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
PPE35 2168858 p.Ser585Arg missense_variant 0.29
PPE35 2168876 p.Phe579Leu missense_variant 0.6
PPE35 2168882 c.1731T>A synonymous_variant 0.33
PPE35 2169029 p.Asp528Glu missense_variant 0.33
PPE35 2169095 p.Leu506Phe missense_variant 0.33
PPE35 2169264 p.Ser450Thr missense_variant 0.13
PPE35 2169596 p.Phe339Leu missense_variant 0.36
PPE35 2169814 p.Phe267Ile missense_variant 0.22
PPE35 2170265 c.347delG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726261 c.69G>T synonymous_variant 1.0
ahpC 2726463 p.Phe91Ile missense_variant 0.12
ahpC 2726695 p.Leu168His missense_variant 0.14
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 0.97
rpoA 3878493 c.15G>A synonymous_variant 1.0
rpoA 3878664 c.-157A>T upstream_gene_variant 0.5
ddn 3986987 c.144G>T synonymous_variant 0.96
ddn 3987180 p.Asp113Asn missense_variant 1.0
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 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 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0