TB-Profiler result

Run: ERR067732
Summary

Run ID: ERR067732

Sample name:

Date: 31-03-2023 09:07:44

Number of reads: 3607774

Percentage reads mapped: 94.66

Strain: lineage4.1;lineage2.2.1

Drug-resistance: RR-TB

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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
lineage2 East-Asian Beijing RD105 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.88
lineage4.1 Euro-American T;X;H None 0.86
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.12
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.08
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
rpoB 761095 p.Leu430Pro missense_variant 0.14 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.14 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.65 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2289016 p.Thr76Pro missense_variant 0.22 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.45 kanamycin
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
ccsA 620625 p.Ile245Met missense_variant 0.1
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 0.93
rpoC 766645 p.Glu1092Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776094 p.Arg796His missense_variant 0.9
mmpL5 776100 p.Thr794Ile missense_variant 0.11
mmpL5 776182 p.Asp767Asn missense_variant 0.1
mmpL5 777310 p.Gly391Ser missense_variant 0.85
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.1
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.35
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.37
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.16
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.26
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.24
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.24
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.18
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.1
rrs 1473261 n.1416G>A non_coding_transcript_exon_variant 0.1
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.25
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102632 c.410delG frameshift_variant 0.87
katG 2154724 p.Arg463Leu missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 0.19
PPE35 2169320 p.Leu431Phe missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289356 c.-115G>C upstream_gene_variant 0.84
ahpC 2726338 p.Val49Gly missense_variant 0.32
ribD 2987307 p.Ala157Pro missense_variant 0.21
thyA 3073806 c.666C>G synonymous_variant 0.2
thyA 3073949 p.Pro175Ser missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449117 p.Ala205Glu missense_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474774 c.768G>C synonymous_variant 0.9
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.93
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15
alr 3841505 c.-85C>T upstream_gene_variant 0.88
clpC1 4038857 c.1848C>A synonymous_variant 0.38
embC 4239842 c.-21C>A upstream_gene_variant 0.27
embC 4240225 c.363G>T synonymous_variant 0.93
embC 4242425 p.Arg855Gly missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.9
embB 4249408 c.2895G>A synonymous_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.16