TB-Profiler result

Run: SRR19417260
Summary

Run ID: SRR19417260

Sample name:

Date: 03-04-2023 21:37:44

Number of reads: 532371

Percentage reads mapped: 99.62

Strain: lineage4.2.2.2;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.76
lineage4 Euro-American LAM;T;S;X;H None 0.12
lineage4.2 Euro-American H;T;LAM None 0.13
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.54
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.76
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8842 p.Glu514Ala missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491080 p.Arg100Gly missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.87
mshA 575577 c.231delG frameshift_variant 0.12
mshA 576077 c.730C>T synonymous_variant 0.28
rpoB 759746 c.-61C>T upstream_gene_variant 0.88
rpoB 762174 p.Val790Phe missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 0.69
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775817 c.2664T>C synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.11
mmpS5 779622 c.-717T>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305100 p.Asn724Asp missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473349 n.1504G>A non_coding_transcript_exon_variant 0.12
rrl 1473418 n.-240G>A upstream_gene_variant 0.12
rrl 1473428 n.-229_-228delGG upstream_gene_variant 0.11
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.11
rrl 1475306 n.1650delT non_coding_transcript_exon_variant 0.13
inhA 1674465 c.264C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918151 p.Val71Asp missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 0.94
katG 2156010 c.102A>G synonymous_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.12
PPE35 2170461 p.Gly51Glu missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.76
pncA 2289365 c.-125delC upstream_gene_variant 0.83
pncA 2289626 c.-385G>C upstream_gene_variant 0.11
pncA 2289837 c.-596T>C upstream_gene_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 0.83
ahpC 2726534 c.342C>T synonymous_variant 0.45
folC 2746523 c.1075delG frameshift_variant 0.13
ribD 2986952 c.114C>T synonymous_variant 0.13
ribD 2987259 c.421T>C synonymous_variant 0.18
ribD 2987418 p.Gly194Ser missense_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.11
thyX 3067347 p.Ala200Asp missense_variant 0.11
thyX 3067522 p.Thr142Ala missense_variant 0.1
thyX 3067657 c.289C>A synonymous_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087483 p.Ala222Thr missense_variant 0.11
fbiD 3338946 c.-172C>T upstream_gene_variant 0.15
Rv3083 3448337 c.-167C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.12
fbiA 3641283 p.Ile247Met missense_variant 0.12
fbiB 3642537 p.Val335Met missense_variant 0.1
embC 4240172 p.Val104Met missense_variant 0.47
embC 4241562 p.Arg567His missense_variant 0.79
embC 4242075 p.Arg738Gln missense_variant 0.7
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244822 c.1590G>T synonymous_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 0.15
embA 4246212 p.Ser994Thr missense_variant 0.11
embB 4246472 c.-42T>C upstream_gene_variant 0.12
embB 4247071 c.561_562dupGG frameshift_variant 0.11
ubiA 4269947 c.-114G>A upstream_gene_variant 0.11
ethA 4326953 p.Asp174Gly missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407927 p.Glu92Asp missense_variant 0.12
gid 4408124 p.Ala27Pro missense_variant 0.14
gid 4408344 c.-142T>A upstream_gene_variant 0.12