TB-Profiler result

Run: SRR18911120
Summary

Run ID: SRR18911120

Sample name:

Date: 03-04-2023 20:40:37

Number of reads: 141299

Percentage reads mapped: 96.33

Strain:

Drug-resistance: HR-TB

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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
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
katG 2154494 c.1617delC frameshift_variant 0.29 isoniazid
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 6023 p.Lys262Glu missense_variant 0.25
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6418 c.-884C>T upstream_gene_variant 0.2
gyrB 6980 p.Ala581Thr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoB 759689 c.-118A>G upstream_gene_variant 0.29
rpoB 759708 c.-99G>A upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765338 p.Gln657Glu missense_variant 0.29
rpoC 766621 c.3253delC frameshift_variant 0.18
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
fbiC 1303160 p.Gly77Glu missense_variant 0.29
fbiC 1304339 p.Phe470Ser missense_variant 0.22
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406834 c.507C>T synonymous_variant 0.67
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461003 c.-42A>G upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471752 n.-94G>T upstream_gene_variant 0.33
rrs 1472291 n.446G>A non_coding_transcript_exon_variant 0.4
rrs 1472398 n.553T>C non_coding_transcript_exon_variant 0.22
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.67
rrl 1475597 n.1940G>A non_coding_transcript_exon_variant 0.4
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.4
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1918441 p.Val168Phe missense_variant 0.25
ndh 2102380 c.663G>T synonymous_variant 0.33
ndh 2103225 c.-183A>C upstream_gene_variant 0.6
katG 2154049 p.Lys688Met missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155230 p.Glu294Asp missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288767 p.Leu159Met missense_variant 0.67
pncA 2288927 c.315C>A synonymous_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.75
kasA 2518606 c.492G>C synonymous_variant 0.67
kasA 2518609 p.Met165Ile missense_variant 0.67
kasA 2519048 p.Gly312Ser missense_variant 1.0
ribD 2987381 p.Gln181His missense_variant 0.25
Rv2752c 3065176 p.Ser339* stop_gained 0.5
Rv2752c 3065262 p.Glu310Asp missense_variant 0.33
Rv2752c 3065802 p.Glu130Asp missense_variant 1.0
Rv2752c 3066997 c.-809_-807delTCG upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640597 p.Val19Ile missense_variant 0.2
ddn 3986734 c.-109delT upstream_gene_variant 0.4
ddn 3986745 c.-98delG upstream_gene_variant 0.22
ddn 3987127 p.Asn95Thr missense_variant 0.29
clpC1 4039714 p.Tyr331His missense_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247639 p.Ala376Thr missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326226 c.1248C>A synonymous_variant 0.29
ethR 4327435 c.-114T>A upstream_gene_variant 0.22
ethA 4327452 p.Val8Ile missense_variant 0.25
whiB6 4338361 p.Arg54Gln missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0