TB-Profiler result

Run: SRR1173311
Summary

Run ID: SRR1173311

Sample name:

Date: 03-04-2023 03:21:29

Number of reads: 918164

Percentage reads mapped: 37.65

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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 0.85
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.85
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.93
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
gyrB 6742 p.Glu501Asp missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.8 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.69 isoniazid
katG 2155135 p.Thr326Met missense_variant 0.13 isoniazid
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.29 pyrazinamide
pncA 2288847 p.Gly132Ala missense_variant 0.91 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.91 ethambutol
ethA 4326855 p.Arg207Gly missense_variant 0.79 ethionamide
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 8948 c.1647G>A synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491021 p.Arg80Leu missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575528 p.Gly61Cys missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 0.92
mshA 576334 c.987G>T synonymous_variant 0.14
mshA 576473 p.Gly376Trp missense_variant 0.25
ccsA 619860 c.-31A>C upstream_gene_variant 0.14
ccsA 620156 p.Gly89Val missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.75
rpoB 759746 c.-61C>T upstream_gene_variant 0.23
rpoB 761240 p.Cys478* stop_gained 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766003 c.2634G>T synonymous_variant 0.15
rpoC 766008 p.Val880Ala missense_variant 0.12
rpoC 766284 p.Thr972Asn missense_variant 0.18
rpoC 766645 p.Glu1092Asp missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.86
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800619 c.-190G>A upstream_gene_variant 0.17
fbiC 1305040 p.Ser704Thr missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472063 n.218C>T non_coding_transcript_exon_variant 0.22
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.29
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.29
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.29
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.33
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.33
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.22
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.22
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.27
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.23
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.27
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.17
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.13
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.2
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.2
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.19
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.15
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.15
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.15
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.21
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.23
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.21
rrl 1474715 n.1060_1061delAA non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.19
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.19
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.23
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.13
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.25
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.2
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.18
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154182 p.Gly644Cys missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168601 p.Gly671Val missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073715 p.Pro253Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448627 p.Gly42Ser missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613249 c.-133A>T upstream_gene_variant 0.18
fbiA 3640986 p.Asp148Glu missense_variant 0.17
fbiB 3642044 c.510G>A synonymous_variant 0.15
clpC1 4039740 p.Ala322Gly missense_variant 0.11
clpC1 4040575 p.Val44Phe missense_variant 0.18
embC 4240817 p.Thr319Ser missense_variant 0.25
embC 4240831 c.969T>G synonymous_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 0.73
embA 4245015 p.Ile595Phe missense_variant 0.13
embB 4246238 c.-276T>G upstream_gene_variant 0.11
embB 4248939 p.Pro809His missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268072 c.764delT frameshift_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0