TB-Profiler result

Run: SRR1181314
Summary

Run ID: SRR1181314

Sample name:

Date: 03-04-2023 04:50:55

Number of reads: 5124713

Percentage reads mapped: 98.54

Strain: lineage4.1.2;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 0.54
lineage1 Indo-Oceanic EAI RD239 0.43
lineage4.1 Euro-American T;X;H None 0.5
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.46
lineage4.1.2 Euro-American T;H None 0.52
lineage1.2.2.1 Indo-Oceanic NA RD239 0.49
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 0.44
gyrB 6112 p.Met291Ile missense_variant 0.48
gyrA 7323 p.Pro8Ala missense_variant 0.57
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.49
gyrA 9143 c.1842T>C synonymous_variant 0.53
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.4
fgd1 491591 p.Lys270Met missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 0.49
ccsA 620659 p.Arg257Cys missense_variant 0.41
rpoB 760115 c.309C>T synonymous_variant 0.55
rpoC 763031 c.-339T>C upstream_gene_variant 0.52
rpoC 763884 p.Ala172Val missense_variant 0.48
rpoC 763886 c.517C>A synonymous_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 0.53
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.45
mmpL5 776659 p.Asp608Asn missense_variant 0.53
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.59
embR 1417019 p.Cys110Tyr missense_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 0.46
PPE35 2168501 p.Phe704Leu missense_variant 0.47
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.52
kasA 2518132 c.18C>T synonymous_variant 0.5
ahpC 2726051 c.-142G>A upstream_gene_variant 0.48
thyX 3068115 c.-170C>T upstream_gene_variant 0.49
thyA 3074034 c.438T>C synonymous_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.55
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.5
fprA 3474679 p.Ile225Val missense_variant 0.48
fprA 3475159 p.Asn385Asp missense_variant 0.55
rpoA 3878381 c.127C>T synonymous_variant 0.42
clpC1 4040517 p.Val63Ala missense_variant 0.5
embC 4240671 p.Thr270Ile missense_variant 0.5
embC 4240750 c.888C>T synonymous_variant 0.53
embC 4241042 p.Asn394Asp missense_variant 0.52
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.65
embA 4243290 p.Ser20Ala missense_variant 0.65
embA 4245969 p.Pro913Ser missense_variant 0.45
embB 4247121 p.Ser203Leu missense_variant 0.62
embB 4247646 p.Glu378Ala missense_variant 0.42
aftB 4268852 c.-16G>A upstream_gene_variant 0.49
ubiA 4269387 p.Glu149Asp missense_variant 0.55
aftB 4269606 c.-770T>C upstream_gene_variant 0.35
ethA 4326439 p.Asn345Lys missense_variant 0.39
ethR 4327450 c.-99G>A upstream_gene_variant 0.46
whiB6 4338215 p.Gly103Cys missense_variant 0.49
whiB6 4338374 p.Lys50Glu missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.49
gid 4407588 c.615A>G synonymous_variant 0.46
gid 4407873 c.330G>T synonymous_variant 0.45
gid 4408397 c.-195A>G upstream_gene_variant 0.47