TB-Profiler result

Run: SRR1183047

Summary

Run ID: SRR1183047

Sample name:

Date: 03-04-2023 04:59:53

Number of reads: 1934110

Percentage reads mapped: 92.59

Strain: lineage2.2;lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.56
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.07
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
gyrA 7570 p.Ala90Val missense_variant 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.21 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.56 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 0.58 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.31 kanamycin, amikacin
embB 4247574 p.Asp354Ala missense_variant 0.56 ethambutol
ethA 4326855 p.Arg207Gly missense_variant 0.24 ethionamide
ethA 4327480 c.-7T>C upstream_gene_variant 0.44 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
gyrB 6112 p.Met291Ile missense_variant 0.26
gyrB 6124 c.885C>T synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.24
gyrA 9304 p.Gly668Asp missense_variant 0.85
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 575750 p.Gly135Trp missense_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620213 p.Gly108Val missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.5
rpoB 760490 c.684C>T synonymous_variant 0.33
rpoB 761327 c.1521A>G synonymous_variant 0.13
rpoB 761345 c.1539G>T synonymous_variant 0.14
rpoB 761360 c.1554T>C synonymous_variant 0.1
rpoB 761362 p.Ser519Thr missense_variant 0.11
rpoB 761457 p.Pro551Ser missense_variant 0.17
rpoB 761465 c.1659G>A synonymous_variant 0.17
rpoB 761471 c.1665C>T synonymous_variant 0.18
rpoB 761477 c.1671C>T synonymous_variant 0.18
rpoB 761492 c.1686G>C synonymous_variant 0.2
rpoB 761504 c.1698C>G synonymous_variant 0.2
rpoB 761510 c.1704T>C synonymous_variant 0.21
rpoB 761531 c.1725C>G synonymous_variant 0.25
rpoB 761537 c.1731C>G synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.63
rpoC 764041 p.Ser224Arg missense_variant 0.13
rpoC 764441 p.Ile358Val missense_variant 0.12
rpoC 764840 p.Ile491Val missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 0.15
rpoC 765385 p.Met672Ile missense_variant 0.17
rpoC 765846 p.Asn826Thr missense_variant 0.5
rpoC 766645 p.Glu1092Asp missense_variant 0.57
rpoC 767037 p.Ala1223Val missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.73
mmpL5 776182 p.Asp767Asn missense_variant 0.58
mmpL5 776395 p.Phe696Leu missense_variant 0.22
mmpL5 779211 c.-731C>A upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 0.94
fbiC 1305339 c.2409C>A synonymous_variant 0.14
Rv1258c 1406218 p.Gly375* stop_gained 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.56
embR 1417019 p.Cys110Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.11
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 0.45
rpsA 1834720 c.1179C>A synonymous_variant 0.13
rpsA 1834838 p.Glu433* stop_gained 0.17
rpsA 1834978 c.1437C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 0.83
ndh 2102215 p.Trp276Cys missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 0.66
katG 2156317 c.-206C>T upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170204 p.Glu137Gln missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.93
pncA 2289940 c.-699C>G upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 0.18
kasA 2518222 c.108G>T synonymous_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 0.13
folC 2746893 p.Arg236Ser missense_variant 0.14
ribD 2986827 c.-12G>A upstream_gene_variant 0.57
ald 3086788 c.-32T>C upstream_gene_variant 0.88
Rv3083 3448400 c.-104G>T upstream_gene_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.81
fprA 3474597 c.591C>A synonymous_variant 0.27
fprA 3475159 p.Asn385Asp missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.39
fbiB 3640692 c.-843C>T upstream_gene_variant 0.14
fbiB 3641409 c.-126G>T upstream_gene_variant 0.12
fbiB 3641442 c.-93G>T upstream_gene_variant 0.12
fbiB 3641990 p.Met152Ile missense_variant 0.5
fbiB 3641994 p.Arg154Cys missense_variant 0.5
fbiB 3642420 c.886C>A synonymous_variant 0.14
alr 3841072 p.Gly117Ser missense_variant 0.29
clpC1 4038535 p.Arg724Ser missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.16
clpC1 4040856 c.-152G>T upstream_gene_variant 0.18
embC 4242175 c.2313G>A synonymous_variant 0.12
embA 4242568 c.-665C>T upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.6
embA 4243554 p.Arg108Ser missense_variant 1.0
embA 4243739 c.507G>A synonymous_variant 0.22
embA 4243796 c.564C>T synonymous_variant 0.12
embA 4243848 p.Val206Met missense_variant 0.31
embB 4247646 p.Glu378Ala missense_variant 0.25
embB 4247941 p.Leu476Phe missense_variant 0.15
embB 4247947 c.1434G>A synonymous_variant 0.15
embB 4249660 c.3148_3150dupGCC conservative_inframe_insertion 0.23
embB 4249771 c.3258C>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.44
aftB 4268928 c.-92C>T upstream_gene_variant 0.15
ubiA 4269124 p.Ala237Val missense_variant 0.18
aftB 4269375 c.-539G>A upstream_gene_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.23
aftB 4269606 c.-770T>C upstream_gene_variant 0.14
ethA 4328196 c.-723G>T upstream_gene_variant 0.13
whiB6 4338224 p.Glu100* stop_gained 0.18
whiB6 4338563 c.-42G>T upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 0.78
whiB6 4338603 c.-82C>T upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 0.74
gid 4407857 p.Arg116Trp missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 0.33
gid 4407927 p.Glu92Asp missense_variant 0.42