TB-Profiler result

Run: ERR036237
Summary

Run ID: ERR036237

Sample name:

Date: 31-03-2023 08:31:14

Number of reads: 1034934

Percentage reads mapped: 97.12

Strain: lineage4.3.4.2.1

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 0.98
lineage4.3 Euro-American (LAM) mainly-LAM None 0.81
lineage4.3.4 Euro-American (LAM) LAM RD174 0.7
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.74
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.83
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 6140 p.Val301Leu missense_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 0.88
gyrA 9304 p.Gly668Asp missense_variant 0.9
mshA 575932 p.Glu195Asp missense_variant 0.43
ccsA 620407 p.Pro173Ala missense_variant 0.4
ccsA 620532 c.642T>G synonymous_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 0.11
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 764725 p.Phe452Leu missense_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.71
rpoC 765150 p.Gly594Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.23
mmpR5 779371 p.Ala128Pro missense_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.18
Rv1258c 1406622 p.Leu240Arg missense_variant 0.15
Rv1258c 1407240 p.Val34Gly missense_variant 0.31
atpE 1461019 c.-26C>A upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.18
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.2
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.25
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.21
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.21
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.14
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.15
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.13
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.22
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.22
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.1
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.15
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.13
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.17
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.2
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.2
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.15
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.15
fabG1 1673449 p.Thr4Pro missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.17
PPE35 2169320 p.Leu431Phe missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.1
eis 2714366 p.Val323Leu missense_variant 0.5
eis 2714787 p.Trp182* stop_gained 0.11
eis 2715586 c.-254G>C upstream_gene_variant 0.67
folC 2746859 p.Ala247Val missense_variant 0.11
folC 2747263 c.336C>A synonymous_variant 0.2
pepQ 2859381 c.1038C>G synonymous_variant 0.42
Rv2752c 3064741 p.Gly484Ala missense_variant 0.33
thyX 3067995 c.-50A>C upstream_gene_variant 0.16
thyA 3073806 c.666C>G synonymous_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.94
fprA 3474601 p.Arg199Gly missense_variant 0.28
whiB7 3568586 p.Thr32Pro missense_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 0.88
fbiB 3641955 p.Gly141Arg missense_variant 0.17
fbiB 3642734 c.1200G>C synonymous_variant 0.3
alr 3840719 c.702A>G synonymous_variant 0.8
rpoA 3878238 p.Asp90Glu missense_variant 0.25
ddn 3987013 p.Gly57Ala missense_variant 0.21
clpC1 4038287 c.2418C>T synonymous_variant 0.76
embC 4242075 p.Arg738Gln missense_variant 0.11
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247126 p.Thr205Ala missense_variant 0.1
embB 4247603 p.Leu364Val missense_variant 0.31
ethA 4327672 c.-199G>A upstream_gene_variant 0.27
whiB6 4338371 p.Thr51Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407991 p.Gly71Val missense_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.84
gid 4408273 c.-71C>G upstream_gene_variant 0.31