TB-Profiler result

Run: ERR2512872
Summary

Run ID: ERR2512872

Sample name:

Date: 31-03-2023 19:18:29

Number of reads: 750985

Percentage reads mapped: 98.67

Strain: lineage4.2.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575401 c.54G>T synonymous_variant 0.12
rpoB 760806 p.Ala334Thr missense_variant 0.11
rpoB 762461 c.2657delA frameshift_variant 0.15
rpoC 764626 c.1257C>A synonymous_variant 0.1
rpoC 764632 c.1263T>C synonymous_variant 0.1
rpoC 764650 c.1281G>T synonymous_variant 0.11
rpoC 764653 c.1284G>C synonymous_variant 0.11
rpoC 764656 c.1287C>T synonymous_variant 0.11
rpoC 764662 c.1293G>C synonymous_variant 0.11
rpoC 764677 c.1308C>G synonymous_variant 0.11
rpoC 764678 p.Lys437Gln missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776168 c.2313C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>G non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474643 n.986A>G non_coding_transcript_exon_variant 1.0
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 1.0
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 1.0
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 1.0
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 1.0
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 1.0
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 1.0
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1475627 n.1970G>T non_coding_transcript_exon_variant 0.67
fabG1 1674036 c.598delC frameshift_variant 0.12
fabG1 1674152 p.Pro238Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102152 c.891C>T synonymous_variant 0.12
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170385 c.228G>T synonymous_variant 0.17
PPE35 2170392 p.Gly74Ala missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.27
ahpC 2726426 c.234C>T synonymous_variant 0.11
thyX 3067540 p.Ala136Thr missense_variant 0.12
ald 3086742 c.-78A>C upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087008 c.189G>A synonymous_variant 0.14
fbiD 3339186 c.69A>G synonymous_variant 0.1
fbiD 3339751 p.Ala212Thr missense_variant 0.11
Rv3083 3449982 c.1479G>C synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613127 c.-12delA upstream_gene_variant 0.18
alr 3840638 c.783C>T synonymous_variant 0.12
rpoA 3878648 c.-141C>A upstream_gene_variant 0.5
clpC1 4039161 p.His515Gly missense_variant 0.11
clpC1 4040043 p.Gly221Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246078 p.Ser949Asn missense_variant 0.12
embB 4246109 c.-405C>A upstream_gene_variant 0.17
embB 4249271 p.Asp920Asn missense_variant 0.11
embB 4249323 p.Ala937Glu missense_variant 0.18
embB 4249658 p.Met1049Leu missense_variant 0.22
embB 4249747 c.3234C>T synonymous_variant 0.17
ubiA 4269373 p.Ser154Trp missense_variant 0.14
ethR 4327569 p.Ser7Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0