TB-Profiler result

Run: SRR998676
Summary

Run ID: SRR998676

Sample name:

Date: 04-04-2023 23:31:01

Number of reads: 1127636

Percentage reads mapped: 99.43

Strain: lineage6.3.1;lineage4.1.2.1

Drug-resistance: Sensitive

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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 0.38
lineage6 West-Africa 2 AFRI_1 RD702 0.66
lineage4.1 Euro-American T;X;H None 0.39
lineage6.3 West-Africa 2 AFRI_1 RD702 0.54
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.64
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.13
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
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 6446 p.Ala403Ser missense_variant 0.67
gyrB 6507 p.Ala423Val missense_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.65
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9656 c.2355C>G synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 0.3
fgd1 491668 p.Lys296Glu missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 0.64
rpoB 760115 c.309C>T synonymous_variant 0.26
rpoB 760671 c.865C>T synonymous_variant 0.67
rpoB 760969 p.Ser388Leu missense_variant 0.82
rpoB 761723 p.Glu639Asp missense_variant 0.62
rpoC 763031 c.-339T>C upstream_gene_variant 0.75
rpoC 765150 p.Gly594Glu missense_variant 0.44
rpoC 766012 c.2643C>G synonymous_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 0.38
mmpL5 776100 p.Thr794Ile missense_variant 0.65
mmpL5 776411 c.2070T>C synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.55
embR 1417341 p.Gly3Arg missense_variant 0.12
embR 1417478 c.-131C>G upstream_gene_variant 0.1
atpE 1461251 c.207G>T synonymous_variant 0.65
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673468 p.Lys10Thr missense_variant 0.38
fabG1 1673609 p.Gly57Asp missense_variant 0.11
inhA 1674434 p.Val78Ala missense_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102694 p.Val117Ile missense_variant 0.62
katG 2154116 p.Ile666Val missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 0.75
katG 2155503 c.609C>T synonymous_variant 0.54
katG 2156007 c.105C>T synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 0.47
PPE35 2168731 p.Pro628Thr missense_variant 0.5
PPE35 2170748 c.-136C>T upstream_gene_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 0.73
Rv1979c 2222852 p.Ala105Thr missense_variant 0.69
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288879 c.363G>A synonymous_variant 0.71
kasA 2518076 c.-39C>T upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 0.6
eis 2714852 c.480delC frameshift_variant 0.12
eis 2714865 c.468C>A synonymous_variant 0.12
ahpC 2726116 c.-77T>C upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.31
ald 3086728 c.-92C>T upstream_gene_variant 0.49
ald 3086788 c.-32T>C upstream_gene_variant 0.97
ald 3087084 c.266delA frameshift_variant 0.7
Rv3083 3449781 c.1278G>A synonymous_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.54
Rv3236c 3612302 p.Thr272Met missense_variant 0.26
rpoA 3877696 p.Thr271Ile missense_variant 0.58
embC 4240671 p.Thr270Ile missense_variant 0.88
embC 4241843 p.Leu661Ile missense_variant 0.58
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.45
embA 4244220 c.988C>T synonymous_variant 0.87
embA 4244379 p.Pro383Ser missense_variant 0.65
embB 4246864 c.351C>T synonymous_variant 0.89
embB 4246877 p.Arg122Cys missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 0.86
embB 4248758 c.2245C>T synonymous_variant 0.12
aftB 4268477 c.360C>T synonymous_variant 0.46
aftB 4269351 c.-515C>T upstream_gene_variant 0.7
ubiA 4269387 p.Glu149Asp missense_variant 0.73
aftB 4269522 c.-686C>T upstream_gene_variant 0.59
aftB 4269606 c.-770T>C upstream_gene_variant 0.71
ethA 4326465 p.Ile337Val missense_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.63