TB-Profiler result

Run: ERR2229388
Summary

Run ID: ERR2229388

Sample name:

Date: 31-03-2023 17:08:57

Number of reads: 580886

Percentage reads mapped: 98.86

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H 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 5942 p.Glu235Lys missense_variant 0.5
gyrB 6049 c.810G>C synonymous_variant 0.67
gyrA 7054 c.-248C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8534 c.1233G>T synonymous_variant 0.13
fgd1 491084 p.Val101Gly missense_variant 0.22
mshA 576673 c.1326G>A synonymous_variant 0.22
ccsA 620099 p.Arg70Pro missense_variant 0.67
rpoB 761148 p.Arg448* stop_gained 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.15
rpoB 761947 p.Leu714Gln missense_variant 0.22
rpoC 764856 p.Val496Ala missense_variant 0.15
rpoC 765761 p.Pro798Thr missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775700 c.2781G>A synonymous_variant 0.33
mmpL5 775703 c.2778A>G synonymous_variant 0.33
mmpL5 775715 c.2766G>A synonymous_variant 0.29
mmpL5 775718 c.2763C>G synonymous_variant 0.29
mmpL5 775726 c.2755C>T synonymous_variant 0.25
mmpL5 775727 c.2754C>G synonymous_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800902 p.Gly32Trp missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473719 n.62G>A non_coding_transcript_exon_variant 0.29
rrl 1473940 n.283A>G non_coding_transcript_exon_variant 0.5
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
rpsA 1833558 p.Val6Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918210 p.Ala91Thr missense_variant 0.2
katG 2153970 p.Asp714Glu missense_variant 0.17
katG 2154388 p.Ser575Leu missense_variant 0.18
katG 2156048 p.Val22Phe missense_variant 0.14
katG 2156361 c.-250G>A upstream_gene_variant 0.29
PPE35 2167715 p.Leu966Phe missense_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.14
PPE35 2167833 p.Leu927Arg missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169192 p.Ala474Glu missense_variant 0.2
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.78
PPE35 2170053 p.Thr187Ser missense_variant 0.83
PPE35 2170345 p.Ala90Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518537 c.423C>T synonymous_variant 0.33
kasA 2518809 p.Lys232Arg missense_variant 0.33
eis 2714150 p.Pro395Thr missense_variant 0.12
folC 2747452 c.147G>T synonymous_variant 0.29
Rv2752c 3065422 p.Arg257Gln missense_variant 0.18
ald 3087135 p.Ala106Ser missense_variant 0.18
ald 3087611 c.792G>A synonymous_variant 0.2
fbiA 3640377 c.-166G>T upstream_gene_variant 0.2
fbiA 3640811 p.Gln90Arg missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.23
alr 3841582 c.-162A>G upstream_gene_variant 0.14
alr 3841584 c.-164C>A upstream_gene_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.19
rpoA 3877826 p.Glu228Gln missense_variant 0.33
ddn 3986960 c.117C>A synonymous_variant 0.17
ddn 3987252 p.Gln137Lys missense_variant 0.15
clpC1 4040741 c.-37G>A upstream_gene_variant 0.22
embC 4239778 c.-85C>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245015 p.Ile595Phe missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.44
embB 4246567 c.54G>T synonymous_variant 0.45
embB 4246987 p.Phe158Leu missense_variant 0.29
embB 4249230 p.Gly906Val missense_variant 0.14
aftB 4268418 p.Glu140Gly missense_variant 0.4
ubiA 4269356 p.Arg160Cys missense_variant 0.33
whiB6 4338341 p.Leu61Met missense_variant 0.14
whiB6 4338349 p.Arg58His missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338607 c.-86C>T upstream_gene_variant 0.25