TB-Profiler result

Run: ERR2229708

Summary

Run ID: ERR2229708

Sample name:

Date: 31-03-2023 17:28:23

Number of reads: 976512

Percentage reads mapped: 99.0

Strain: lineage4.8

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
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
katG 2154955 c.1156delG frameshift_variant 0.14 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 6243 p.Arg335Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7707 p.Pro136Thr missense_variant 0.13
fgd1 491371 p.Gly197Ser missense_variant 0.15
rpoC 762524 c.-846G>A upstream_gene_variant 0.15
rpoC 766598 p.Tyr1077His missense_variant 0.11
rpoC 767187 p.Gln1273Pro missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775721 p.Ile920Val missense_variant 0.12
mmpL5 776397 p.Val695Ala missense_variant 0.1
mmpL5 776402 c.2079C>G synonymous_variant 0.11
mmpL5 776405 c.2076T>G synonymous_variant 0.11
mmpL5 776847 p.Gln545Arg missense_variant 0.15
mmpL5 777115 p.Met456Leu missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777126 p.Ser452Ala missense_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpL5 777140 c.1341G>C synonymous_variant 0.2
mmpS5 779676 c.-771C>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304180 p.Leu417Pro missense_variant 0.12
fbiC 1304214 c.1284C>T synonymous_variant 0.11
Rv1258c 1406456 c.885T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472535 n.690C>T non_coding_transcript_exon_variant 0.17
rrs 1473156 n.1311A>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475820 n.2163C>A non_coding_transcript_exon_variant 0.14
rrl 1476212 n.2555T>A non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
fabG1 1673770 p.Ala111Thr missense_variant 0.14
inhA 1673796 c.-406G>C upstream_gene_variant 0.12
fabG1 1674097 p.Val220Leu missense_variant 0.14
rpsA 1834369 c.828C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918256 p.Ala106Asp missense_variant 0.12
katG 2154217 p.Arg632His missense_variant 0.13
katG 2154888 c.1224C>T synonymous_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.57
Rv1979c 2222000 p.Val389Met missense_variant 0.2
Rv1979c 2223135 c.30G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714845 p.Val163Asp missense_variant 0.15
folC 2746437 p.Asp388Tyr missense_variant 0.14
pepQ 2859606 c.813G>T synonymous_variant 0.15
pepQ 2860606 c.-188C>T upstream_gene_variant 0.14
Rv2752c 3065861 c.331C>T synonymous_variant 0.11
thyX 3067499 c.447G>A synonymous_variant 0.2
fprA 3474883 p.Glu293Lys missense_variant 0.2
fprA 3474914 p.Ala303Glu missense_variant 0.25
Rv3236c 3612905 p.Leu71Ser missense_variant 0.1
alr 3841546 c.-126C>A upstream_gene_variant 0.2
rpoA 3878599 c.-92C>G upstream_gene_variant 0.8
rpoA 3878639 c.-132C>G upstream_gene_variant 0.67
clpC1 4038170 c.2535G>A synonymous_variant 0.12
panD 4044280 c.2T>A start_lost 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245367 p.Arg712Leu missense_variant 0.12
embA 4246380 p.Trp1050Arg missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.54
embB 4246556 p.Ala15Pro missense_variant 0.54
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54_55insT frameshift_variant 0.2
ubiA 4269608 p.Arg76Cys missense_variant 0.11
ethA 4326075 p.Leu467Ile missense_variant 0.12
ethA 4327150 p.Asp108Glu missense_variant 0.11
ethA 4327496 c.-23C>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407660 c.543G>A synonymous_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0