TB-Profiler result

Run: ERR2229414
Summary

Run ID: ERR2229414

Sample name:

Date: 31-03-2023 17:10:05

Number of reads: 801351

Percentage reads mapped: 99.18

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6828 p.Met530Lys missense_variant 0.17
gyrB 7118 p.Asp627Tyr missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7382 p.Ser27Arg missense_variant 0.18
gyrA 7407 p.Ile36Phe missense_variant 0.17
gyrA 9707 c.2406G>T synonymous_variant 0.14
fgd1 491347 p.Gly189Arg missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775955 p.Ile842Val missense_variant 0.25
mmpL5 777157 c.1324C>A synonymous_variant 0.25
mmpL5 777164 c.1317C>T synonymous_variant 0.2
mmpR5 779182 p.Gly65Trp missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800951 p.Ser48Ile missense_variant 0.13
fbiC 1303584 c.654C>A synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303798 p.Val290Met missense_variant 0.17
fbiC 1305206 p.Pro759His missense_variant 0.15
embR 1416750 p.Glu200* stop_gained 0.14
embR 1416871 c.477C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473027 n.1182G>T non_coding_transcript_exon_variant 0.12
rrs 1473219 n.1374T>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474711 n.1054G>T non_coding_transcript_exon_variant 0.2
rrl 1475029 n.1377delG non_coding_transcript_exon_variant 0.25
rrl 1475096 n.1439A>T non_coding_transcript_exon_variant 0.33
rrl 1475101 n.1444T>C non_coding_transcript_exon_variant 0.2
rrl 1475628 n.1971G>A non_coding_transcript_exon_variant 0.25
rrl 1476778 n.3121G>T non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
rpsA 1833714 p.Lys58Arg missense_variant 0.17
rpsA 1833869 p.Glu110Gln missense_variant 0.29
rpsA 1834879 c.1338C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918693 p.Ser252Pro missense_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.18
ndh 2102899 c.144T>C synonymous_variant 0.15
katG 2155557 c.555C>T synonymous_variant 0.12
PPE35 2167745 c.2868C>G synonymous_variant 0.12
PPE35 2167760 c.2853G>A synonymous_variant 0.17
PPE35 2167763 p.Ile950Val missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.33
PPE35 2167967 c.2646A>C synonymous_variant 0.33
PPE35 2168054 c.2559G>T synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.22
PPE35 2169030 p.Asp528Val missense_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.4
PPE35 2169281 c.1332T>G synonymous_variant 0.35
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169597 p.Phe339Cys missense_variant 0.12
PPE35 2169717 p.Asn299Ile missense_variant 0.19
PPE35 2169725 c.888T>C synonymous_variant 0.15
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170392 p.Gly74Ala missense_variant 0.17
PPE35 2170400 c.213G>C synonymous_variant 0.18
Rv1979c 2221907 p.Val420Ile missense_variant 0.14
Rv1979c 2222583 c.582A>G synonymous_variant 0.15
Rv1979c 2222972 p.Phe65Ile missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517930 c.-185A>G upstream_gene_variant 0.22
kasA 2518315 c.201G>C synonymous_variant 0.15
kasA 2519153 p.Ile347Val missense_variant 0.18
pepQ 2859525 c.892_893dupGT frameshift_variant 0.29
ribD 2986825 c.-14C>T upstream_gene_variant 0.13
Rv2752c 3065751 p.Asn147Lys missense_variant 0.25
thyX 3067340 c.606G>A synonymous_variant 0.18
thyX 3067459 p.Arg163Cys missense_variant 0.25
thyA 3074264 p.Gly70Cys missense_variant 0.14
ald 3087442 p.Asp208Gly missense_variant 0.12
whiB7 3568512 c.168G>T synonymous_variant 0.12
Rv3236c 3612004 c.1113C>A synonymous_variant 0.12
fbiB 3642174 p.Val214Leu missense_variant 0.2
fbiB 3642196 p.Gly221Val missense_variant 0.18
rpoA 3878691 c.-184G>T upstream_gene_variant 0.18
clpC1 4039031 c.1674T>C synonymous_variant 0.13
clpC1 4039498 p.Ile403Val missense_variant 0.29
clpC1 4039508 c.1197G>C synonymous_variant 0.22
clpC1 4039594 p.Arg371Gly missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4040458 p.Arg83Cys missense_variant 0.18
embC 4240848 p.Asp329Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242997 c.-236G>A upstream_gene_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.5
embB 4247905 c.1392G>T synonymous_variant 0.22
embB 4248496 c.1983G>A synonymous_variant 0.29
embB 4249093 c.2580G>T synonymous_variant 0.17
embB 4249751 c.3238T>C synonymous_variant 0.15
aftB 4268380 p.Trp153Arg missense_variant 0.18
ubiA 4268948 p.Gly296Trp missense_variant 0.29
ethA 4326495 p.Leu327Met missense_variant 0.13
ethR 4326934 c.-615C>A upstream_gene_variant 0.13
ethR 4326937 c.-612G>C upstream_gene_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.21
ethR 4326964 c.-585G>A upstream_gene_variant 0.21
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
ethA 4327818 c.-345A>T upstream_gene_variant 0.17
ethR 4328111 p.Ala188Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408144 p.Arg20Gln missense_variant 0.17
gid 4408289 c.-87T>C upstream_gene_variant 0.25