TB-Profiler result

Run: SRR3675242
Summary

Run ID: SRR3675242

Sample name:

Date: 04-04-2023 05:24:17

Number of reads: 1577892

Percentage reads mapped: 95.54

Strain: lineage3

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 1.0
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620839 p.Leu317Val missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762467 c.-903C>A upstream_gene_variant 0.13
rpoB 762808 p.Lys1001Arg missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
fabG1 1673810 p.Ser124Trp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169293 c.1320T>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288755 p.Val163Leu missense_variant 0.12
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289803 c.-562G>T upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064545 c.1643_1646dupAGCC frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448907 p.Tyr135Ser missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474108 p.Met34Ile missense_variant 0.12
Rv3236c 3612179 p.Ala313Asp missense_variant 0.17
Rv3236c 3612429 p.Ala230Ser missense_variant 0.13
embC 4240622 p.Ala254Ser missense_variant 0.12
embC 4240655 p.Ala265Pro missense_variant 0.19
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244854 p.Val541Ala missense_variant 0.11
embA 4245603 p.Gly791Trp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0