TB-Profiler result

Run: SRR15661598
Summary

Run ID: SRR15661598

Sample name:

Date: 03-04-2023 14:21:32

Number of reads: 1824173

Percentage reads mapped: 99.57

Strain: lineage2.2.1.1

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 1.0
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
tlyA 1918335 c.397dupC frameshift_variant 1.0 capreomycin, capreomycin
pncA 2288935 p.Tyr103Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7763 c.462T>A synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576100 p.Asp251Glu missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.12
mshA 576456 p.Val370Gly missense_variant 0.18
mshA 576616 c.1269G>C synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779127 c.139_140dupGA frameshift_variant 0.51
mmpR5 779204 p.Arg72Gln missense_variant 0.41
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472429 n.584T>C non_coding_transcript_exon_variant 0.12
rrs 1472560 n.715G>C non_coding_transcript_exon_variant 0.14
rrs 1472562 n.717C>T non_coding_transcript_exon_variant 0.14
rrs 1472932 n.1087C>A non_coding_transcript_exon_variant 0.14
rrl 1473395 n.-263G>C upstream_gene_variant 0.18
rrl 1473626 n.-32C>G upstream_gene_variant 0.18
rrl 1473638 n.-20T>C upstream_gene_variant 0.29
rrl 1473712 n.55G>T non_coding_transcript_exon_variant 0.2
rrl 1473770 n.113T>A non_coding_transcript_exon_variant 0.14
rrl 1474430 n.773C>A non_coding_transcript_exon_variant 0.14
rrl 1474563 n.906G>T non_coding_transcript_exon_variant 0.12
rrl 1475127 n.1470G>C non_coding_transcript_exon_variant 0.25
rrl 1475148 n.1491G>C non_coding_transcript_exon_variant 0.25
rrl 1475667 n.2010G>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170047 p.Leu189Gly missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170059 p.Val185Gly missense_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
pepQ 2860119 c.299delA frameshift_variant 0.12
pepQ 2860153 p.Glu89Ala missense_variant 0.15
pepQ 2860159 p.Ala87Gly missense_variant 0.42
thyA 3074513 c.-42C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.22
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339746 p.Ala210Gly missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.17
whiB7 3568428 c.252A>G synonymous_variant 0.33
whiB7 3568432 p.Arg83Leu missense_variant 0.11
whiB7 3568437 c.243T>C synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878636 c.-129C>G upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.31
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248319 c.1806A>T synonymous_variant 0.16
embB 4248324 p.Ala604Gly missense_variant 0.37
embB 4248328 c.1815G>C synonymous_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267828 p.Arg337Trp missense_variant 0.12
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