TB-Profiler result

Run: SRR19428540
Summary

Run ID: SRR19428540

Sample name:

Date: 03-04-2023 21:39:40

Number of reads: 810444

Percentage reads mapped: 99.58

Strain: lineage4.2.2.2;lineage3.1.1;lineage1

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 0.4
lineage4 Euro-American LAM;T;S;X;H None 0.44
lineage1 Indo-Oceanic EAI RD239 0.06
lineage4.2 Euro-American H;T;LAM None 0.39
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.57
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.42
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.44
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.35
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 8688 p.Ala463Ser missense_variant 0.4
gyrA 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.58
mshA 576077 c.730C>T synonymous_variant 0.35
ccsA 620625 p.Ile245Met missense_variant 0.28
rpoB 759746 c.-61C>T upstream_gene_variant 0.33
rpoB 761489 c.1683G>A synonymous_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 0.56
rpoC 767094 p.Ser1242Asn missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.59
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.62
PPE35 2167926 p.Leu896Ser missense_variant 0.43
PPE35 2168971 p.Ile548Val missense_variant 0.45
PPE35 2170461 p.Gly51Glu missense_variant 0.44
Rv1979c 2222308 p.Asp286Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.37
pncA 2289365 c.-125delC upstream_gene_variant 0.43
ahpC 2726051 c.-142G>A upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 0.46
ahpC 2726534 c.342C>T synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17
Rv2752c 3065711 p.Gly161Ser missense_variant 0.12
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.57
ald 3086742 c.-78A>C upstream_gene_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.14
Rv3236c 3612009 p.Ala370Thr missense_variant 0.23
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11
embC 4240172 p.Val104Met missense_variant 0.19
embC 4241562 p.Arg567His missense_variant 0.53
embC 4242075 p.Arg738Gln missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.12
ethA 4326953 p.Asp174Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.5
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0