TB-Profiler result

Run: SRR6964661
Summary

Run ID: SRR6964661

Sample name:

Date: 04-04-2023 18:20:47

Number of reads: 480582

Percentage reads mapped: 99.66

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 7316 c.15G>A synonymous_variant 0.12
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 491014 p.Thr78Pro missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760356 p.Thr184Ala missense_variant 0.33
rpoB 760476 p.Arg224Cys missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764605 c.1238delT frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777820 c.661C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781774 p.His72Arg missense_variant 0.17
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.83
embR 1416808 c.540C>T synonymous_variant 0.18
embR 1416989 c.358delA frameshift_variant 0.13
atpE 1461086 c.42A>G synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834722 c.1184delG frameshift_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.26
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Thr missense_variant 1.0
PPE35 2168651 p.Leu654Phe missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714138 p.Ala399Thr missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746727 p.Leu291* stop_gained 0.17
pepQ 2860399 p.Arg7Gln missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086835 p.Pro6Ser missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640534 c.-9T>C upstream_gene_variant 0.2
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244457 p.Ala409Thr missense_variant 1.0
embA 4245948 p.Gln906* stop_gained 0.13
embB 4248422 p.Ala637Thr missense_variant 0.11
aftB 4268576 c.261C>T synonymous_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0