TB-Profiler result

Run: SRR5341243
Summary

Run ID: SRR5341243

Sample name:

Date: 04-04-2023 10:10:21

Number of reads: 1617730

Percentage reads mapped: 99.38

Strain: lineage2.2.1;lineage1.2.2.2

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
lineage2 East-Asian Beijing RD105 0.78
lineage1 Indo-Oceanic EAI RD239 0.1
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.79
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.19
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.78
lineage1.2.2.2 Indo-Oceanic NA RD239 0.17
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 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 0.14 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
pncA 2288997 p.His82Arg missense_variant 0.26 pyrazinamide
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 8452 p.Ala384Val missense_variant 0.13
gyrA 8685 p.Ile462Val missense_variant 0.7
gyrA 9143 c.1842T>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.95
mshA 575907 p.Ala187Val missense_variant 0.81
ccsA 620625 p.Ile245Met missense_variant 0.79
ccsA 620748 c.858T>G synonymous_variant 0.26
rpoB 759615 c.-192A>C upstream_gene_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.14
rpoC 763886 c.517C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.87
mmpS5 779615 c.-710C>G upstream_gene_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
fbiC 1303016 p.Val29Gly missense_variant 0.24
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473694 n.37C>T non_coding_transcript_exon_variant 0.12
rrl 1475284 n.1627C>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918645 p.Asn236Asp missense_variant 0.26
ndh 2102240 p.Arg268His missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168279 c.2334G>T synonymous_variant 0.12
PPE35 2168742 p.Gly624Asp missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.56
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27
Rv1979c 2222936 p.Ala77Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.28
thyX 3067467 p.Ala160Val missense_variant 0.91
thyX 3068145 c.-200C>A upstream_gene_variant 0.66
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.22
fprA 3475375 c.1360_1361insGA frameshift_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68
clpC1 4040517 p.Val63Ala missense_variant 0.12
clpC1 4040719 c.-15A>G upstream_gene_variant 0.25
embC 4241042 p.Asn394Asp missense_variant 0.17
embC 4241551 c.1689A>G synonymous_variant 0.2
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 0.66
embA 4245969 p.Pro913Ser missense_variant 0.3
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4247496 c.984delT frameshift_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.7
aftB 4267960 p.Val293Met missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 0.23
aftB 4269606 c.-770T>C upstream_gene_variant 0.13
ethA 4326148 c.1326G>T synonymous_variant 0.16
ethA 4326439 p.Asn345Lys missense_variant 0.2
ethR 4327617 p.Asp23Glu missense_variant 0.16
whiB6 4338203 p.Arg107Cys missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.22
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.79