TB-Profiler result

Run: ERR4553409
Summary

Run ID: ERR4553409

Sample name:

Date: 01-04-2023 06:08:56

Number of reads: 1210934

Percentage reads mapped: 99.54

Strain: lineage4

Drug-resistance: MDR-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
lineage4 Euro-American LAM;T;S;X;H None 0.09
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.91
lineage1.2.2.2 Indo-Oceanic NA RD239 0.91
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
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.67 para-aminosalicylic_acid
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 0.94
gyrB 6112 p.Met291Ile missense_variant 0.75
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.93
gyrA 8452 p.Ala384Val missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 0.83
fgd1 491742 c.960T>C synonymous_variant 0.79
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.86
rpoC 763886 c.517C>A synonymous_variant 0.29
rpoC 764449 c.1080G>T synonymous_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.85
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.92
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289082 p.Pro54Ser missense_variant 0.96
kasA 2518132 c.18C>T synonymous_variant 0.93
ahpC 2726051 c.-142G>A upstream_gene_variant 0.5
Rv2752c 3064889 p.Lys435Glu missense_variant 0.96
thyX 3067949 c.-4C>T upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
fprA 3474597 c.591C>A synonymous_variant 0.4
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 1.0
Rv3236c 3613221 c.-105C>T upstream_gene_variant 0.97
alr 3841546 c.-126C>A upstream_gene_variant 0.7
alr 3841568 c.-148G>A upstream_gene_variant 0.57
alr 3841570 c.-151delA upstream_gene_variant 0.57
alr 3841574 c.-154T>G upstream_gene_variant 0.57
alr 3841578 c.-158G>T upstream_gene_variant 0.57
alr 3841582 c.-162A>G upstream_gene_variant 0.57
alr 3841584 c.-164C>A upstream_gene_variant 0.57
alr 3841589 c.-170delG upstream_gene_variant 0.57
clpC1 4040517 p.Val63Ala missense_variant 0.29
clpC1 4040556 p.Glu50Val missense_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 0.93
embC 4241042 p.Asn394Asp missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.29
embB 4247468 p.Tyr319Asp missense_variant 0.91
embB 4247646 p.Glu378Ala missense_variant 0.2
embB 4249441 c.2928A>G synonymous_variant 0.9
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
ethA 4326439 p.Asn345Lys missense_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.8
whiB6 4338635 c.-114A>C upstream_gene_variant 0.83
gid 4407588 c.615A>G synonymous_variant 0.79
gid 4407873 c.330G>T synonymous_variant 0.4
gid 4407994 p.Ser70Ile missense_variant 0.94