TB-Profiler result

Run: SRR3085283
Summary

Run ID: SRR3085283

Sample name:

Date: 04-04-2023 04:56:53

Number of reads: 905316

Percentage reads mapped: 99.31

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7848 p.Val183Phe missense_variant 0.13
gyrA 9333 p.Gly678Trp missense_variant 0.12
fgd1 490771 c.-12T>G upstream_gene_variant 0.22
rpoB 760021 p.Gly72Val missense_variant 0.22
rpoB 760711 c.907delG frameshift_variant 0.17
rpoC 763526 p.Gly53Trp missense_variant 0.12
rpoC 764972 p.Asp535Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776580 p.Leu634Gln missense_variant 0.15
mmpL5 777214 p.Ala423Thr missense_variant 0.14
mmpL5 777747 p.Gly245Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801062 p.Arg85Gln missense_variant 0.17
rplC 801133 p.Gly109Cys missense_variant 0.15
fbiC 1305449 p.Ile840Asn missense_variant 0.12
embR 1417066 p.Leu94Phe missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473314 n.1469A>C non_coding_transcript_exon_variant 0.14
rrl 1473767 n.110G>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.91
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
fabG1 1673585 p.Ser49Tyr missense_variant 0.33
fabG1 1673840 p.Arg134Leu missense_variant 0.14
inhA 1674300 c.99C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102484 p.Gly187* stop_gained 0.15
ndh 2102616 p.Asp143Tyr missense_variant 0.18
katG 2154142 p.Phe657Ser missense_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 0.94
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.68
PPE35 2170302 p.Met104Thr missense_variant 1.0
Rv1979c 2222449 p.Ala239Glu missense_variant 0.15
Rv1979c 2222517 c.648C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517998 c.-117C>A upstream_gene_variant 0.11
kasA 2518147 c.33C>T synonymous_variant 0.27
folC 2746832 p.Val256Gly missense_variant 0.18
pepQ 2859437 p.Val328Ile missense_variant 0.14
ribD 2986847 p.Asp3Glu missense_variant 0.14
Rv2752c 3065868 c.324C>A synonymous_variant 0.14
thyA 3074331 c.141C>A synonymous_variant 0.12
whiB7 3568831 c.-152C>A upstream_gene_variant 0.15
fbiB 3641634 p.Ala34Ser missense_variant 0.13
clpC1 4040567 c.138C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242948 p.Gly1029Val missense_variant 0.15
embC 4243016 p.Asp1052Tyr missense_variant 0.14
embA 4243588 p.Arg119Leu missense_variant 0.14
embA 4245804 p.Gln858* stop_gained 0.12
embA 4246200 p.Gln990Lys missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Leu missense_variant 0.2
embB 4248392 p.Ala627Ser missense_variant 0.15
embB 4249354 c.2841G>C synonymous_variant 1.0
ubiA 4268930 p.Gly302Cys missense_variant 0.4
aftB 4269246 c.-410G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0