TB-Profiler result

Run: SRR18002889
Summary

Run ID: SRR18002889

Sample name:

Date: 03-04-2023 19:07:58

Number of reads: 734332

Percentage reads mapped: 92.14

Strain: lineage4.8;lineage2.2

Drug-resistance: MDR-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
lineage4 Euro-American LAM;T;S;X;H None 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.05
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.91
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 761460 p.Arg552Cys missense_variant 0.89 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289105 p.Ala46Val missense_variant 0.2 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.9 ethambutol
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 6084 p.Gly282Asp missense_variant 0.75
gyrB 6129 p.Tyr297Cys missense_variant 0.2
gyrB 6599 p.Glu454Lys missense_variant 0.12
gyrB 6674 p.Leu479Ile missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7605 p.Pro102Ala missense_variant 0.18
fgd1 491437 p.Asp219Tyr missense_variant 0.12
fgd1 491446 p.Val222Ile missense_variant 0.13
fgd1 491505 c.723G>A synonymous_variant 0.12
mshA 575378 p.Gly11Arg missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576372 p.Ala342Val missense_variant 0.12
ccsA 620679 c.789C>T synonymous_variant 0.18
ccsA 620782 p.Ala298Thr missense_variant 0.14
rpoB 759809 c.3G>A start_lost 0.15
rpoB 759962 c.156C>T synonymous_variant 0.12
rpoB 760784 c.978G>A synonymous_variant 0.15
rpoB 761845 p.Gln680Arg missense_variant 0.11
rpoB 761988 p.Ala728Thr missense_variant 0.15
rpoB 762179 c.2373C>T synonymous_variant 0.4
rpoC 763991 p.Ile208Val missense_variant 0.12
rpoC 765073 c.1704G>A synonymous_variant 0.14
rpoC 767299 c.3930C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776700 p.Ile594Thr missense_variant 0.15
mmpL5 778789 c.-309G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781731 p.Thr58Ala missense_variant 0.11
rplC 801062 p.Arg85Gln missense_variant 0.14
fbiC 1304289 p.Ile453Met missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.33
rrs 1473325 n.1480G>A non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 1.0
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.6
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.4
inhA 1673363 c.-839G>A upstream_gene_variant 0.14
fabG1 1673704 p.Ala89Thr missense_variant 0.12
rpsA 1833469 c.-73G>A upstream_gene_variant 0.29
rpsA 1833574 c.33A>G synonymous_variant 0.12
rpsA 1833735 p.Ala65Val missense_variant 0.12
rpsA 1833796 p.Glu85Asp missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.12
rpsA 1834459 c.918G>A synonymous_variant 0.17
rpsA 1834684 c.1143C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918664 p.Trp242* stop_gained 0.13
katG 2154300 c.1812G>A synonymous_variant 0.15
katG 2154886 p.Ala409Val missense_variant 0.18
katG 2155317 c.795G>T synonymous_variant 0.22
katG 2155445 p.Val223Met missense_variant 0.11
PPE35 2167651 c.2962T>C stop_lost&splice_region_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168200 p.Ala805Pro missense_variant 1.0
PPE35 2170105 p.Leu170Phe missense_variant 0.13
Rv1979c 2222966 c.197_198delCG frameshift_variant 0.22
Rv1979c 2223009 c.156T>A synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289813 c.-572G>A upstream_gene_variant 0.11
pncA 2289818 c.-577T>C upstream_gene_variant 0.11
eis 2715148 p.Ala62Glu missense_variant 0.12
eis 2715306 c.27C>T synonymous_variant 0.18
ahpC 2726708 c.516G>A synonymous_variant 0.12
folC 2746537 c.1062C>T synonymous_variant 0.17
folC 2747686 c.-88C>T upstream_gene_variant 0.11
pepQ 2859410 p.Arg337Gly missense_variant 0.18
pepQ 2860022 p.Glu133Lys missense_variant 0.14
pepQ 2860326 c.93A>T synonymous_variant 0.22
pepQ 2860402 p.Arg6His missense_variant 0.13
ribD 2987120 c.282C>T synonymous_variant 0.11
Rv2752c 3065707 p.Ala162Val missense_variant 0.13
thyA 3074502 c.-31C>T upstream_gene_variant 0.11
ald 3087104 c.285G>A synonymous_variant 0.15
ald 3087664 p.Thr282Ile missense_variant 0.13
ald 3087722 c.906delC frameshift_variant 0.15
Rv3083 3448357 c.-147C>A upstream_gene_variant 0.14
whiB7 3568673 p.Val3Ile missense_variant 0.11
whiB7 3568763 c.-85delT upstream_gene_variant 0.12
Rv3236c 3612018 p.Pro367Ser missense_variant 0.15
Rv3236c 3612235 c.882G>A synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
fbiB 3641088 c.-447G>A upstream_gene_variant 0.15
fbiB 3642808 p.Ala425Val missense_variant 0.2
alr 3840959 c.462G>C synonymous_variant 0.15
alr 3841460 c.-40G>T upstream_gene_variant 0.12
ddn 3986657 c.-187C>T upstream_gene_variant 0.13
ddn 3987192 p.Glu117Lys missense_variant 0.12
clpC1 4038795 p.Ser637Asn missense_variant 0.12
clpC1 4039244 c.1461G>T synonymous_variant 0.2
clpC1 4039274 c.1431G>C synonymous_variant 0.17
clpC1 4039852 p.Phe285Leu missense_variant 0.17
clpC1 4040455 p.Ala84Thr missense_variant 0.12
embC 4239920 p.Arg20Cys missense_variant 0.11
embC 4239941 p.Arg27Trp missense_variant 0.12
embC 4241466 p.Phe535Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243240 p.His3Leu missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 0.27
embA 4245314 c.2084_2085delTG frameshift_variant 0.13
embA 4245825 p.Asp865Asn missense_variant 1.0
embB 4247363 p.Ile284Val missense_variant 0.14
embB 4248779 p.Glu756Lys missense_variant 0.14
embB 4248855 p.Gly781Asp missense_variant 0.12
aftB 4267393 p.Pro482Ser missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.29
aftB 4267913 c.924G>A synonymous_variant 0.13
aftB 4268717 c.120C>T synonymous_variant 0.14
aftB 4269144 c.-308C>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.38
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0