TB-Profiler result

Run: ERR1950029

Summary

Run ID: ERR1950029

Sample name:

Date: 31-03-2023 15:37:58

Number of reads: 717205

Percentage reads mapped: 99.4

Strain: lineage4.8

Drug-resistance: Other


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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
ethA 4327301 p.Asp58Ala missense_variant 0.2 ethionamide
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 6416 p.Thr393Pro missense_variant 0.2
gyrB 6700 p.Asn487Lys missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7694 p.Glu131Asp missense_variant 0.57
gyrA 8286 p.Asn329Tyr missense_variant 0.33
fgd1 491219 p.Asp146Ala missense_variant 0.29
mshA 576642 p.Asn432Thr missense_variant 0.33
rpoB 760032 p.Pro76Thr missense_variant 0.22
rpoB 761376 p.Tyr524His missense_variant 0.17
rpoC 762533 c.-837T>A upstream_gene_variant 0.26
rpoB 762993 p.Gly1063Trp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.14
mmpL5 779319 c.-839T>A upstream_gene_variant 0.4
mmpL5 779328 c.-848T>C upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801099 c.291T>A synonymous_variant 0.27
fbiC 1303512 c.582T>G synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416623 p.Asp242Ala missense_variant 0.36
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472013 n.168A>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474407 n.750A>T non_coding_transcript_exon_variant 0.21
rrl 1475182 n.1525T>A non_coding_transcript_exon_variant 0.22
rrl 1475605 n.1948A>G non_coding_transcript_exon_variant 0.14
inhA 1674521 p.Pro107Gln missense_variant 0.2
inhA 1674617 p.Asn139Thr missense_variant 0.18
rpsA 1834074 p.Lys178Met missense_variant 0.18
rpsA 1834941 p.Asp467Ala missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918058 p.Val40Gly missense_variant 0.18
ndh 2102657 p.Asp129Ala missense_variant 0.2
ndh 2102904 p.Thr47Ala missense_variant 0.33
katG 2154187 p.Pro642Leu missense_variant 0.15
PPE35 2168206 c.2406delT frameshift_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169594 p.Gly340Val missense_variant 0.5
PPE35 2169793 p.Asn274Tyr missense_variant 0.29
PPE35 2170499 p.Leu38Phe missense_variant 0.25
Rv1979c 2221900 p.Ile422Ser missense_variant 0.18
Rv1979c 2223033 c.132A>C synonymous_variant 0.15
Rv1979c 2223212 c.-48A>T upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289900 c.-659A>C upstream_gene_variant 0.38
pncA 2289958 c.-717T>A upstream_gene_variant 0.67
pncA 2290019 c.-778A>C upstream_gene_variant 0.23
pncA 2290040 c.-799A>C upstream_gene_variant 0.18
eis 2714917 p.Glu139Val missense_variant 0.22
eis 2715060 p.His91Gln missense_variant 0.15
folC 2746377 p.Ser408Ala missense_variant 0.33
folC 2746755 p.Leu282Ile missense_variant 0.25
pepQ 2860110 c.309G>T synonymous_variant 0.21
ribD 2987345 p.Asp169Glu missense_variant 0.14
Rv2752c 3065295 p.Gln299His missense_variant 0.25
Rv2752c 3065638 p.Leu185Pro missense_variant 0.14
thyX 3067470 p.Asn159Thr missense_variant 0.29
thyA 3074318 p.Phe52Ile missense_variant 0.29
ald 3087226 p.Val136Gly missense_variant 0.15
ald 3087247 p.Gln143Leu missense_variant 0.15
fbiD 3339334 p.Ala73Ser missense_variant 0.18
whiB7 3568640 p.Arg14* stop_gained 0.23
whiB7 3568754 c.-75T>A upstream_gene_variant 0.18
fbiA 3640655 p.Asp38Ala missense_variant 0.6
fbiB 3641602 p.Phe23Ser missense_variant 0.33
alr 3841415 p.Lys2Asn missense_variant 0.2
rpoA 3877852 p.Phe219Cys missense_variant 0.25
rpoA 3877855 p.Leu218Trp missense_variant 0.25
rpoA 3877861 p.Val216Gly missense_variant 0.22
ddn 3987065 c.222T>A synonymous_variant 0.27
clpC1 4040031 p.Val225Gly missense_variant 0.22
panD 4044084 c.198T>C synonymous_variant 0.12
embC 4239739 c.-124A>C upstream_gene_variant 0.12
embC 4239879 p.Ala6Gly missense_variant 0.22
embC 4240307 p.Gly149Cys missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246534 p.Arg7Ser missense_variant 0.22
embB 4247028 p.Leu172Gln missense_variant 0.29
aftB 4267075 p.Leu588Ile missense_variant 0.17
aftB 4267473 p.Gly455Asp missense_variant 0.15
aftB 4267704 p.Leu378Arg missense_variant 0.22
aftB 4267756 p.Lys361* stop_gained 0.33
aftB 4267857 p.Ile327Asn missense_variant 0.2
ubiA 4269140 p.Cys232Gly missense_variant 0.33
ethA 4326458 p.Ile339Asn missense_variant 0.25
ethA 4326629 p.Phe282Cys missense_variant 0.19
ethA 4327307 p.Asp56Ala missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407797 p.Ser136Ala missense_variant 0.2
gid 4407829 p.Gln125Leu missense_variant 0.25
gid 4408006 p.Val66Gly missense_variant 0.18
gid 4408313 c.-111A>C upstream_gene_variant 0.33
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0