TB-Profiler result

Run: ERR161123
Summary

Run ID: ERR161123

Sample name:

Date: 31-03-2023 14:47:00

Number of reads: 4179442

Percentage reads mapped: 99.36

Strain: lineage4.3.4.2.1;lineage1.2.2.1

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 0.18
lineage1 Indo-Oceanic EAI RD239 0.82
lineage4.3 Euro-American (LAM) mainly-LAM None 0.19
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.85
lineage4.3.4 Euro-American (LAM) LAM RD174 0.18
lineage1.2.2.1 Indo-Oceanic NA RD239 0.81
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.17
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.19
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 5075 c.-165C>T upstream_gene_variant 0.84
gyrB 6112 p.Met291Ile missense_variant 0.72
gyrB 6140 p.Val301Leu missense_variant 0.28
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.79
gyrA 9143 c.1842T>C synonymous_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.81
fgd1 491742 c.960T>C synonymous_variant 0.8
ccsA 620659 p.Arg257Cys missense_variant 0.79
rpoC 763031 c.-339T>C upstream_gene_variant 0.83
rpoC 763884 p.Ala172Val missense_variant 0.79
rpoC 763886 c.517C>A synonymous_variant 0.79
rpoC 764995 c.1626C>G synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776311 p.Gly724Ser missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.89
embR 1417019 p.Cys110Tyr missense_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.83
rrl 1474517 n.860C>T non_coding_transcript_exon_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.77
PPE35 2167926 p.Leu896Ser missense_variant 0.98
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.82
ahpC 2726051 c.-142G>A upstream_gene_variant 0.77
Rv2752c 3064761 c.1431C>T synonymous_variant 0.15
Rv2752c 3064852 p.Met447Thr missense_variant 0.77
thyA 3073806 c.666C>G synonymous_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 0.22
thyA 3074553 c.-82C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.23
Rv3083 3448714 p.Asp71His missense_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.91
fprA 3475159 p.Asn385Asp missense_variant 0.76
Rv3236c 3612009 p.Ala370Thr missense_variant 0.17
Rv3236c 3612865 p.Ser84Arg missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 0.2
clpC1 4038857 c.1848C>A synonymous_variant 0.28
clpC1 4040517 p.Val63Ala missense_variant 0.83
embC 4239842 c.-21C>A upstream_gene_variant 0.26
embC 4240671 p.Thr270Ile missense_variant 0.82
embC 4240750 c.888C>T synonymous_variant 0.81
embC 4241042 p.Asn394Asp missense_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245321 p.Met697Val missense_variant 0.79
embA 4245969 p.Pro913Ser missense_variant 0.8
embB 4247646 p.Glu378Ala missense_variant 0.78
aftB 4267517 c.1320A>G synonymous_variant 0.76
ubiA 4269387 p.Glu149Asp missense_variant 0.79
aftB 4269606 c.-770T>C upstream_gene_variant 0.89
ethA 4326439 p.Asn345Lys missense_variant 0.82
ethR 4327450 c.-99G>A upstream_gene_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.85
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407873 c.330G>T synonymous_variant 0.71
gid 4408156 p.Leu16Arg missense_variant 0.22