TB-Profiler result

Run: SRR1180225
Summary

Run ID: SRR1180225

Sample name:

Date: 03-04-2023 03:53:30

Number of reads: 1960548

Percentage reads mapped: 92.55

Strain: lineage2.2.1;lineage1.1

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
lineage1 Indo-Oceanic EAI RD239 0.09
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.06
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.56
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 0.42 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.15 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.43 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 0.53 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.31 kanamycin, amikacin
embB 4247574 p.Asp354Ala missense_variant 0.5 ethambutol
ethA 4326855 p.Arg207Gly missense_variant 0.17 ethionamide
ethA 4327480 c.-7T>C upstream_gene_variant 0.52 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 0.28
gyrB 6124 c.885C>T synonymous_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.94
gyrA 8452 p.Ala384Val missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 0.84
fgd1 490861 p.Ala27Thr missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.9
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576071 p.Val242Leu missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.42
rpoB 760490 c.684C>T synonymous_variant 0.2
rpoB 761145 p.Arg447Cys missense_variant 0.17
rpoB 761327 c.1521A>G synonymous_variant 0.14
rpoB 761345 c.1539G>T synonymous_variant 0.14
rpoB 761360 c.1554T>C synonymous_variant 0.11
rpoB 761362 p.Ser519Thr missense_variant 0.11
rpoB 761374 p.Val523Glu missense_variant 0.12
rpoB 761504 c.1698C>G synonymous_variant 0.15
rpoB 761510 c.1704T>C synonymous_variant 0.15
rpoB 761531 c.1725C>G synonymous_variant 0.17
rpoB 761537 c.1731C>G synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.75
rpoC 763694 p.Gly109Cys missense_variant 0.15
rpoC 763886 c.517C>A synonymous_variant 0.2
rpoC 765171 p.Pro601Leu missense_variant 0.15
rpoC 765846 p.Asn826Thr missense_variant 0.38
rpoC 766645 p.Glu1092Asp missense_variant 0.41
rpoC 766661 p.Val1098Met missense_variant 0.11
rpoC 766960 c.3591C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.7
mmpL5 776182 p.Asp767Asn missense_variant 0.52
mmpL5 776395 p.Phe696Leu missense_variant 0.23
mmpL5 777376 p.Glu369* stop_gained 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 0.94
rpsL 781585 p.Arg9Leu missense_variant 0.13
rplC 800920 p.Arg38Ser missense_variant 0.12
fbiC 1304133 c.1203G>T synonymous_variant 0.4
fbiC 1304935 c.2006dupC frameshift_variant 0.11
fbiC 1305339 c.2409C>A synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.59
embR 1417019 p.Cys110Tyr missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1475999 n.2342G>T non_coding_transcript_exon_variant 0.12
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
rpsA 1833343 c.-199G>T upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.39
rpsA 1834838 p.Glu433* stop_gained 0.2
tlyA 1917893 c.-47G>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 0.86
tlyA 1917980 p.Arg14Gln missense_variant 0.29
tlyA 1918372 p.Gly145Ser missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 0.52
katG 2154852 p.Met420Ile missense_variant 0.13
katG 2155115 p.Leu333Ile missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.79
PPE35 2170048 p.Leu189Val missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.9
pncA 2289940 c.-699C>G upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 0.2
kasA 2518693 c.579C>G synonymous_variant 0.2
kasA 2518702 c.588C>T synonymous_variant 0.18
kasA 2519321 p.Gly403Arg missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 0.16
folC 2746421 p.Ala393Glu missense_variant 0.15
ribD 2986827 c.-12G>A upstream_gene_variant 0.52
ribD 2987392 p.Arg185Leu missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.15
Rv2752c 3065305 p.Ala296Val missense_variant 0.14
Rv2752c 3067005 c.-814C>A upstream_gene_variant 0.18
thyA 3073715 p.Pro253Ala missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.86
Rv3083 3448714 p.Asp71His missense_variant 0.3
Rv3083 3449069 p.Ala189Val missense_variant 0.13
fprA 3473870 c.-137C>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.82
fprA 3474597 c.591C>A synonymous_variant 0.13
fprA 3475103 p.Gly366Val missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44
fbiB 3642420 c.886C>A synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 0.12
clpC1 4038535 p.Arg724Ser missense_variant 0.12
clpC1 4038857 c.1848C>A synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.19
embC 4242175 c.2313G>A synonymous_variant 0.2
embA 4242568 c.-665C>T upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.43
embA 4243739 c.507G>A synonymous_variant 0.15
embA 4243848 p.Val206Met missense_variant 0.27
embB 4247527 c.1014G>C synonymous_variant 0.11
embB 4247539 c.1026T>C synonymous_variant 0.12
embB 4247550 p.Ala346Asp missense_variant 0.11
embB 4247554 c.1041T>C synonymous_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 0.5
embB 4247947 c.1434G>A synonymous_variant 0.13
embB 4249771 c.3258C>T synonymous_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.5
ubiA 4269124 p.Ala237Val missense_variant 0.23
aftB 4269375 c.-539G>A upstream_gene_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.17
ethA 4328196 c.-723G>T upstream_gene_variant 0.12
whiB6 4338563 c.-42G>T upstream_gene_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 0.92
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407857 p.Arg116Trp missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 0.38
gid 4407927 p.Glu92Asp missense_variant 0.47
gid 4408070 p.Trp45Arg missense_variant 0.16