TB-Profiler result

Run: SRR11972358
Summary

Run ID: SRR11972358

Sample name:

Date: 03-04-2023 05:38:20

Number of reads: 1690664

Percentage reads mapped: 81.16

Strain: lineage3.1.2;lineage1.2.2

Drug-resistance: Other

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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 0.65
lineage1 Indo-Oceanic EAI RD239 0.35
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.43
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.41
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.67
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
gyrB 6735 p.Asn499Thr missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrB 6742 p.Glu501Asp missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
ethA 4326419 c.1054delG frameshift_variant 0.3 ethionamide, ethionamide
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 0.39
gyrB 6112 p.Met291Ile missense_variant 0.56
gyrA 7268 c.-34C>T upstream_gene_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7884 p.Arg195Cys missense_variant 0.42
gyrA 8452 p.Ala384Val missense_variant 0.34
gyrA 9143 c.1842T>C synonymous_variant 0.37
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.62
rpoC 762434 c.-936T>G upstream_gene_variant 0.47
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.44
rpoC 763886 c.517C>A synonymous_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471820 n.-25delC upstream_gene_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918162 p.Glu75Lys missense_variant 0.34
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155269 c.843C>T synonymous_variant 0.37
PPE35 2167772 c.2841C>T synonymous_variant 0.62
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.64
PPE35 2168742 p.Gly624Asp missense_variant 0.47
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.69
pncA 2289365 c.-125delC upstream_gene_variant 0.77
kasA 2518132 c.18C>T synonymous_variant 0.46
ahpC 2725929 c.-264C>G upstream_gene_variant 0.62
ahpC 2726051 c.-142G>A upstream_gene_variant 0.34
ahpC 2726105 c.-88G>A upstream_gene_variant 0.57
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.32
fprA 3475159 p.Asn385Asp missense_variant 0.25
Rv3236c 3612784 c.332delT frameshift_variant 0.12
Rv3236c 3612984 p.Asn45His missense_variant 0.49
rpoA 3878632 c.-125C>A upstream_gene_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 0.34
embC 4240671 p.Thr270Ile missense_variant 0.31
embC 4241042 p.Asn394Asp missense_variant 0.41
embC 4242075 p.Arg738Gln missense_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245789 p.Thr853Ala missense_variant 0.63
embA 4245969 p.Pro913Ser missense_variant 0.56
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.15
embB 4246556 p.Ala15Pro missense_variant 0.15
embB 4246979 p.Gly156Ser missense_variant 0.34
embB 4247646 p.Glu378Ala missense_variant 0.27
ubiA 4269387 p.Glu149Asp missense_variant 0.41
aftB 4269606 c.-770T>C upstream_gene_variant 0.27
ethA 4326148 c.1326G>T synonymous_variant 0.41
ethA 4326439 p.Asn345Lys missense_variant 0.34
ethR 4327694 p.Asp49Ala missense_variant 0.13
whiB6 4338203 p.Arg107Cys missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.35
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.53