TB-Profiler result

Run: ERR4553882
Summary

Run ID: ERR4553882

Sample name:

Date: 01-04-2023 06:24:01

Number of reads: 1607492

Percentage reads mapped: 99.54

Strain:

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.96
lineage1.2.2.2 Indo-Oceanic NA RD239 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
gyrA 7582 p.Asp94Ala missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288731 p.Ala171Thr missense_variant 0.94 pyrazinamide
embB 4249512 p.Met1000Arg missense_variant 0.94 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491359 p.Ile193Leu missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576482 p.Val379Leu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.5
rpoC 763886 c.517C>A synonymous_variant 0.5
rpoC 767011 c.3642G>C synonymous_variant 0.97
rpoC 767123 p.Val1252Leu missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473817 n.160T>C non_coding_transcript_exon_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2221725 c.1440T>G synonymous_variant 0.93
Rv1979c 2222308 p.Asp286Gly missense_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
pepQ 2860159 p.Ala87Gly missense_variant 0.18
Rv2752c 3064889 p.Lys435Glu missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.4
Rv3083 3448391 c.-113C>T upstream_gene_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.5
alr 3841546 c.-126C>A upstream_gene_variant 0.94
alr 3841568 c.-148G>A upstream_gene_variant 0.86
alr 3841570 c.-151delA upstream_gene_variant 0.8
alr 3841574 c.-154T>G upstream_gene_variant 0.8
alr 3841578 c.-158G>T upstream_gene_variant 0.8
alr 3841582 c.-162A>G upstream_gene_variant 0.8
alr 3841584 c.-164C>A upstream_gene_variant 0.8
alr 3841589 c.-170delG upstream_gene_variant 0.8
alr 3841612 c.-193_-192insC upstream_gene_variant 0.75
embC 4240671 p.Thr270Ile missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.93
embB 4246542 p.Ser10Asn missense_variant 0.18
embB 4246584 p.Arg24Pro missense_variant 0.53
ubiA 4269387 p.Glu149Asp missense_variant 0.67
aftB 4269606 c.-770T>C upstream_gene_variant 0.55
ethA 4326439 p.Asn345Lys missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.55
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.83
gid 4407979 p.Pro75Leu missense_variant 1.0