TB-Profiler result

Run: ERR9787223
Summary

Run ID: ERR9787223

Sample name:

Date: 02-04-2023 13:05:18

Number of reads: 3996827

Percentage reads mapped: 88.85

Strain: lineage6.3.1

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
lineage6 West-Africa 2 AFRI_1 RD702 0.99
lineage6.3 West-Africa 2 AFRI_1 RD702 0.99
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.99
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
gyrB 6446 p.Ala403Ser missense_variant 0.93
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491668 p.Lys296Glu missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619862 c.-29G>A upstream_gene_variant 1.0
rpoB 760424 c.618C>G synonymous_variant 0.16
rpoB 760430 c.624T>C synonymous_variant 0.16
rpoB 760475 c.669A>G synonymous_variant 0.17
rpoB 760481 c.675G>C synonymous_variant 0.16
rpoB 760484 c.678A>G synonymous_variant 0.17
rpoB 760969 p.Ser388Leu missense_variant 0.94
rpoB 761723 p.Glu639Asp missense_variant 0.91
rpoB 762338 c.2532T>C synonymous_variant 0.14
rpoC 762410 c.-960T>C upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.17
rpoC 762995 c.-375G>T upstream_gene_variant 0.16
rpoC 763013 c.-357C>G upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763675 c.306C>G synonymous_variant 0.15
rpoC 763774 c.405G>C synonymous_variant 0.14
rpoC 764554 c.1185C>T synonymous_variant 0.14
rpoC 764764 c.1395T>C synonymous_variant 0.15
rpoC 764815 c.1446A>G synonymous_variant 0.15
rpoC 764827 c.1458G>C synonymous_variant 0.15
rpoC 765739 c.2370G>T synonymous_variant 0.14
rpoC 765850 c.2481G>C synonymous_variant 0.15
rpoC 765892 c.2523T>C synonymous_variant 0.15
rpoC 765967 c.2598C>T synonymous_variant 0.14
rpoC 766549 c.3180G>C synonymous_variant 0.15
rpoC 766573 c.3204T>C synonymous_variant 0.16
rpoC 766582 c.3213C>G synonymous_variant 0.14
rpoC 766583 p.Gly1072Ser missense_variant 0.14
rpoC 766588 p.Glu1073Asp missense_variant 0.15
rpoC 766594 c.3225G>C synonymous_variant 0.15
rpoC 766597 c.3228C>G synonymous_variant 0.15
rpoC 766607 p.Ile1080Leu missense_variant 0.16
rpoC 766630 c.3261G>C synonymous_variant 0.16
rpoC 766657 c.3288A>G synonymous_variant 0.18
rpoC 766660 c.3291G>C synonymous_variant 0.17
rpoC 766672 c.3303T>C synonymous_variant 0.18
rpoC 766673 p.Gly1102Asn missense_variant 0.18
rpoC 766726 c.3357T>C synonymous_variant 0.16
rpoC 766738 c.3369G>C synonymous_variant 0.16
rpoC 766861 c.3492G>C synonymous_variant 0.16
rpoC 766864 c.3495G>C synonymous_variant 0.16
rpoC 766876 c.3507C>T synonymous_variant 0.18
rpoC 766882 c.3513C>T synonymous_variant 0.17
rpoC 766900 c.3531T>C synonymous_variant 0.17
rpoC 766933 c.3564A>G synonymous_variant 0.17
rpoC 766945 c.3576A>G synonymous_variant 0.16
rpoC 766963 c.3594T>C synonymous_variant 0.15
rpoC 766972 c.3603G>C synonymous_variant 0.15
rpoC 766996 c.3627C>T synonymous_variant 0.18
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.16
rpoC 767014 c.3645G>C synonymous_variant 0.17
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.18
rpoC 767059 c.3690T>G synonymous_variant 0.16
rpoC 767062 c.3693C>A synonymous_variant 0.16
rpoC 767098 c.3729T>C synonymous_variant 0.15
rpoC 767134 c.3765C>A synonymous_variant 0.14
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 1302899 c.-32A>G upstream_gene_variant 1.0
atpE 1461251 c.207G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.14
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.14
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14
inhA 1674434 p.Val78Ala missense_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102694 p.Val117Ile missense_variant 0.98
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
thyX 3067490 c.456C>G synonymous_variant 0.15
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3449781 c.1278G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841377 p.Thr15Ile missense_variant 1.0
rpoA 3877679 p.Ala277Ser missense_variant 0.15
rpoA 3877696 p.Thr271Ile missense_variant 0.85
rpoA 3877704 c.804G>C synonymous_variant 0.15
rpoA 3878271 c.237T>C synonymous_variant 0.17
rpoA 3878292 c.216T>C synonymous_variant 0.15
rpoA 3878298 c.210A>G synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.16
rpoA 3878310 c.198G>C synonymous_variant 0.16
rpoA 3878313 c.195G>C synonymous_variant 0.16
rpoA 3878322 c.186A>G synonymous_variant 0.16
rpoA 3878331 c.177A>G synonymous_variant 0.15
rpoA 3878337 c.171T>C synonymous_variant 0.15
rpoA 3878346 c.162T>C synonymous_variant 0.16
rpoA 3878364 c.144A>C synonymous_variant 0.15
rpoA 3878367 c.141C>G synonymous_variant 0.15
rpoA 3878376 c.132G>C synonymous_variant 0.17
rpoA 3878385 c.123C>G synonymous_variant 0.16
rpoA 3878388 c.120C>G synonymous_variant 0.16
rpoA 3878391 c.117T>C synonymous_variant 0.17
rpoA 3878415 c.93C>T synonymous_variant 0.18
rpoA 3878424 c.84G>C synonymous_variant 0.17
rpoA 3878436 c.72A>G synonymous_variant 0.16
rpoA 3878442 c.66G>C synonymous_variant 0.16
rpoA 3878454 c.54A>C synonymous_variant 0.15
rpoA 3878639 c.-132C>G upstream_gene_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4244220 c.988C>T synonymous_variant 0.96
embA 4244379 p.Pro383Ser missense_variant 0.96
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268477 c.360C>T synonymous_variant 0.98
ubiA 4268953 p.Thr294Met missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 0.91
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0