TB-Profiler result

Run: ERR2228904

Summary

Run ID: ERR2228904

Sample name:

Date: 31-03-2023 16:25:34

Number of reads: 274585

Percentage reads mapped: 81.88

Strain: lineage4

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
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
rpsL 781815 p.Arg86Trp missense_variant 0.22 streptomycin
ethA 4326807 p.Glu223Lys missense_variant 0.25 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 5146 c.-94A>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8045 c.744C>A synonymous_variant 0.14
gyrA 8859 p.Ile520Val missense_variant 0.25
fgd1 491682 p.Tyr300* stop_gained 0.15
rpoB 761067 p.Ile421Val missense_variant 0.2
rpoB 763119 p.Asn1105Tyr missense_variant 0.22
rpoC 764840 p.Ile491Val missense_variant 0.22
rpoC 766956 p.Glu1196Ala missense_variant 0.67
rpoC 766970 p.Ala1201Ser missense_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776472 p.Gln670Arg missense_variant 0.15
mmpL5 776563 p.Glu640* stop_gained 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781932 c.373T>C stop_lost&splice_region_variant 0.18
fbiC 1305090 c.2160C>T synonymous_variant 0.67
fbiC 1305340 p.Ala804Thr missense_variant 0.33
Rv1258c 1407067 p.Val92Leu missense_variant 0.14
embR 1417258 c.90G>C synonymous_variant 0.4
atpE 1461220 p.Leu59Ser missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475464 n.1807A>G non_coding_transcript_exon_variant 0.4
fabG1 1673271 c.-169G>T upstream_gene_variant 0.2
rpsA 1834041 p.Lys167Met missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167974 p.Ala880Val missense_variant 0.2
PPE35 2168184 p.Thr810Met missense_variant 0.25
PPE35 2168252 c.2361G>A synonymous_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.18
PPE35 2169712 p.Leu301Met missense_variant 0.17
PPE35 2169725 c.888T>C synonymous_variant 0.14
PPE35 2169919 p.Leu232Ile missense_variant 0.18
PPE35 2169923 c.690C>G synonymous_variant 0.18
PPE35 2169932 c.681C>T synonymous_variant 0.22
PPE35 2169939 p.Gly225Ala missense_variant 0.2
PPE35 2169941 c.672C>T synonymous_variant 0.2
PPE35 2169944 c.669G>C synonymous_variant 0.2
PPE35 2169947 c.666T>C synonymous_variant 0.17
PPE35 2169956 c.657T>C synonymous_variant 0.17
PPE35 2169964 p.Leu217Val missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.57
PPE35 2170238 c.375T>G synonymous_variant 0.11
PPE35 2170247 p.Ile122Met missense_variant 0.12
PPE35 2170518 p.Asp32Val missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288898 p.Pro115Gln missense_variant 0.15
ribD 2986890 p.Ser18Arg missense_variant 0.29
Rv2752c 3064608 c.1584G>A synonymous_variant 0.29
thyA 3074037 c.435C>T synonymous_variant 0.29
fprA 3474144 p.Trp46Cys missense_variant 0.12
fbiA 3640356 c.-187G>A upstream_gene_variant 0.17
fbiA 3640955 p.Pro138Leu missense_variant 0.2
fbiA 3641359 p.Gly273Cys missense_variant 0.15
clpC1 4040593 p.Ile38Phe missense_variant 0.18
embC 4240312 c.450G>A synonymous_variant 0.67
embC 4240783 c.921G>A synonymous_variant 0.22
embC 4240843 c.981C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246098 p.Phe956Leu missense_variant 0.25
embB 4249342 c.2829C>A synonymous_variant 0.33
ubiA 4269141 p.Leu231Phe missense_variant 0.33
ethR 4327742 p.Phe65Tyr missense_variant 0.12
whiB6 4338220 p.Arg101Leu missense_variant 0.2
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0