TB-Profiler result

Run: ERR2514178
Summary

Run ID: ERR2514178

Sample name:

Date: 31-03-2023 20:10:07

Number of reads: 528426

Percentage reads mapped: 99.54

Strain: La3

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
La3 M.orygis None None 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
gyrB 5516 p.Ile93Val missense_variant 1.0
gyrB 6109 c.870G>A synonymous_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8930 c.1629C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 1.0
fgd1 490838 p.Glu19Val missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
mshA 575768 p.Ala141Ser missense_variant 0.11
mshA 575798 p.Val151Met missense_variant 0.12
ccsA 619790 c.-101G>A upstream_gene_variant 0.18
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.88
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
mmpL5 776419 p.Ser688Ala missense_variant 0.13
mmpL5 776424 p.Asp686Val missense_variant 0.13
mmpL5 777355 p.Val376Met missense_variant 0.29
mmpL5 778086 c.394dupG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801203 p.Phe132Ser missense_variant 0.13
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1417424 c.-77G>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472015 n.170A>T non_coding_transcript_exon_variant 0.2
rrs 1472763 n.918G>A non_coding_transcript_exon_variant 0.2
rrl 1473869 n.212C>T non_coding_transcript_exon_variant 0.29
rrl 1475303 n.1647delT non_coding_transcript_exon_variant 0.5
rrl 1476664 n.3007T>G non_coding_transcript_exon_variant 1.0
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
inhA 1674860 p.Glu220Gly missense_variant 0.4
rpsA 1833921 p.Lys127Met missense_variant 0.2
rpsA 1834363 c.822G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101930 c.1113C>T synonymous_variant 0.22
ndh 2102240 p.Arg268Leu missense_variant 0.17
katG 2154707 p.Val469Leu missense_variant 1.0
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
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169807 c.805delC frameshift_variant 0.12
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519057 p.Thr315Ser missense_variant 0.12
kasA 2519062 c.948T>G synonymous_variant 0.13
kasA 2519065 c.951C>A synonymous_variant 0.12
kasA 2519070 p.Asp319Val missense_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.14
kasA 2519153 p.Ile347Val missense_variant 0.14
kasA 2519308 c.1194C>T synonymous_variant 0.12
ahpC 2726378 c.186T>A synonymous_variant 1.0
folC 2746391 p.Val403Ala missense_variant 1.0
ribD 2987096 c.258C>T synonymous_variant 0.13
Rv2752c 3065935 p.His86Leu missense_variant 0.11
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
thyX 3067312 p.Ala212Thr missense_variant 0.15
thyX 3067812 p.Gln45Arg missense_variant 1.0
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 3448783 p.Val94Ile missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474998 p.Gly331Asp missense_variant 0.15
fprA 3475113 c.1107G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
fbiA 3640489 c.-54C>T upstream_gene_variant 0.12
fbiB 3641584 p.Val17Ala missense_variant 1.0
clpC1 4039853 c.852G>A synonymous_variant 1.0
panD 4044134 p.Asp50Asn missense_variant 1.0
panD 4044391 c.-110C>A upstream_gene_variant 0.15
embC 4240392 p.Ala177Val missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241180 p.Pro440Ser missense_variant 0.2
embC 4241559 p.Arg566His missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4245995 c.-519G>A upstream_gene_variant 0.11
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4246976 p.Ala155Pro missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338527 c.-6T>C upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338688 c.-167T>C upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0