TB-Profiler result

Run: ERR2228827
Summary

Run ID: ERR2228827

Sample name:

Date: 31-03-2023 16:22:13

Number of reads: 579198

Percentage reads mapped: 99.38

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 5265 p.Gln9Arg missense_variant 0.11
gyrB 5738 p.Thr167Pro missense_variant 0.25
gyrB 6642 p.Lys468Ile missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575416 c.69T>G synonymous_variant 0.25
ccsA 619766 c.-125A>C upstream_gene_variant 0.23
ccsA 620821 p.Asn311Tyr missense_variant 0.33
rpoB 759743 c.-64G>A upstream_gene_variant 0.25
rpoB 760407 p.Ser201Arg missense_variant 0.3
rpoB 760900 p.Asp365Ala missense_variant 0.25
rpoB 761287 p.Leu494Gln missense_variant 0.29
rpoB 762534 p.Ile910Phe missense_variant 0.27
rpoB 762628 p.Asp941Ala missense_variant 0.27
rpoB 762664 p.Leu953Arg missense_variant 0.18
rpoB 762682 p.Glu959Ala missense_variant 0.4
rpoC 765645 p.Gln759Leu missense_variant 0.29
rpoC 766865 p.Thr1166Pro missense_variant 0.27
rpoC 766914 p.Asp1182Ala missense_variant 0.25
rpoC 767174 p.Asn1269Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775837 p.Thr882Pro missense_variant 0.5
mmpL5 777219 p.Leu421Gln missense_variant 0.29
mmpL5 777363 p.Met373Arg missense_variant 0.23
mmpS5 778589 p.Gln106Leu missense_variant 0.29
mmpR5 779080 p.Ser31Cys missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781902 p.Ser115Arg missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406498 p.Leu281Phe missense_variant 0.29
Rv1258c 1406829 p.Ile171Thr missense_variant 0.29
embR 1416661 c.687C>G synonymous_variant 0.2
embR 1416956 p.Phe131Cys missense_variant 0.5
atpE 1461090 p.Ile16Phe missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.5
rrs 1471796 n.-50A>T upstream_gene_variant 0.3
rrs 1472969 n.1124A>T non_coding_transcript_exon_variant 0.4
rrl 1473634 n.-24A>T upstream_gene_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474666 n.1009T>A non_coding_transcript_exon_variant 0.2
rrl 1475067 n.1410A>T non_coding_transcript_exon_variant 0.25
rrl 1475141 n.1484A>T non_coding_transcript_exon_variant 0.29
rrl 1475388 n.1731A>T non_coding_transcript_exon_variant 0.22
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.38
rrl 1476064 n.2407A>T non_coding_transcript_exon_variant 0.4
rrl 1476222 n.2565A>T non_coding_transcript_exon_variant 0.2
rrl 1476230 n.2573A>T non_coding_transcript_exon_variant 0.22
rpsA 1833457 c.-85T>G upstream_gene_variant 0.33
rpsA 1834153 p.Asn204Lys missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918713 p.Asp258Glu missense_variant 0.18
katG 2154332 p.Phe594Ile missense_variant 0.17
katG 2154347 c.1762_1764delGAG conservative_inframe_deletion 0.17
katG 2155261 p.Val284Gly missense_variant 0.29
katG 2155702 p.Asp137Ala missense_variant 0.25
katG 2156405 c.-294T>A upstream_gene_variant 0.4
PPE35 2168359 p.Ser752Cys missense_variant 0.43
PPE35 2168555 p.Phe686Leu missense_variant 0.2
PPE35 2168661 p.Ile651Lys missense_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169053 c.1560T>A synonymous_variant 0.33
PPE35 2169144 p.Val490Glu missense_variant 0.43
PPE35 2169524 p.Asn363Lys missense_variant 0.67
PPE35 2170035 p.Val193Ala missense_variant 0.2
PPE35 2170430 c.183A>T synonymous_variant 0.25
Rv1979c 2221977 p.Leu396Phe missense_variant 0.25
Rv1979c 2222295 p.Lys290Asn missense_variant 0.2
Rv1979c 2222470 p.Phe232Tyr missense_variant 0.2
Rv1979c 2223057 c.108A>T synonymous_variant 0.25
Rv1979c 2223077 p.Ala30Thr missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288996 p.His82Gln missense_variant 0.27
kasA 2518212 p.Trp33Ser missense_variant 0.14
kasA 2518722 p.Glu203Ala missense_variant 0.13
eis 2714566 p.Leu256Gln missense_variant 0.2
eis 2714980 p.Leu118Pro missense_variant 0.13
eis 2715560 c.-228T>C upstream_gene_variant 0.18
ahpC 2726471 p.His93Gln missense_variant 0.43
ahpC 2726608 p.Asp139Ala missense_variant 0.75
folC 2746743 p.Tyr286Asn missense_variant 0.29
folC 2747007 p.Ser198Cys missense_variant 0.25
pepQ 2859678 c.741A>T synonymous_variant 0.31
pepQ 2860174 p.Tyr82Ser missense_variant 0.15
pepQ 2860183 p.Val79Gly missense_variant 0.18
ribD 2987263 p.Val142Gly missense_variant 0.2
Rv2752c 3065149 p.Val348Gly missense_variant 0.67
Rv2752c 3065180 p.Ser338Ala missense_variant 0.4
Rv2752c 3065299 p.Asp298Ala missense_variant 0.67
Rv2752c 3065591 p.Cys201Arg missense_variant 0.25
thyX 3067304 p.Glu214Asp missense_variant 0.43
thyX 3068129 c.-184A>T upstream_gene_variant 0.29
thyA 3074296 p.Leu59Arg missense_variant 0.5
ald 3087705 p.Tyr296Asn missense_variant 0.22
fprA 3474359 p.Asp118Ala missense_variant 0.14
fprA 3474418 p.Phe138Ile missense_variant 0.54
whiB7 3568463 p.Gln73* stop_gained 0.33
Rv3236c 3612128 p.Leu330Arg missense_variant 0.38
Rv3236c 3612414 p.Ser235Ala missense_variant 0.4
Rv3236c 3613063 c.54T>G synonymous_variant 0.25
Rv3236c 3613232 c.-116T>G upstream_gene_variant 0.27
fbiA 3640348 c.-195A>C upstream_gene_variant 0.22
alr 3841092 p.Leu110Arg missense_variant 0.2
alr 3841599 c.-179T>G upstream_gene_variant 0.31
rpoA 3877579 p.Asp310Ala missense_variant 0.15
rpoA 3878298 p.Lys70Asn missense_variant 0.25
clpC1 4038314 c.2391T>G synonymous_variant 0.18
clpC1 4039216 p.Phe497Ile missense_variant 0.2
clpC1 4039360 p.Ser449Gly missense_variant 0.17
clpC1 4039530 p.Asp392Ala missense_variant 0.15
clpC1 4039984 p.Thr241Pro missense_variant 0.33
embC 4240248 p.Asp129Ala missense_variant 0.33
embC 4241043 p.Asn394Thr missense_variant 0.25
embC 4241786 p.Tyr642Asp missense_variant 0.2
embC 4242411 p.Val850Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 0.94
embA 4244746 p.Leu505His missense_variant 0.17
embA 4245457 p.Glu742Ala missense_variant 0.25
embA 4245610 p.Val793Gly missense_variant 0.29
embB 4246589 p.Thr26Pro missense_variant 0.27
embB 4248344 p.Thr611Ser missense_variant 0.2
ubiA 4269037 p.Val266Gly missense_variant 0.27
ubiA 4269997 c.-164C>T upstream_gene_variant 0.22
whiB6 4338223 p.Glu100Ala missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0