TB-Profiler result

Run: ERR2229629
Summary

Run ID: ERR2229629

Sample name:

Date: 31-03-2023 17:22:25

Number of reads: 984365

Percentage reads mapped: 99.07

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6557 p.Gly440Ser missense_variant 0.12
gyrA 7271 c.-31A>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8077 p.Val259Ala missense_variant 0.12
gyrA 9120 p.Arg607Cys missense_variant 0.14
fgd1 491164 c.382C>A synonymous_variant 0.14
mshA 575919 p.Gly191Val missense_variant 0.14
mshA 576567 p.Arg407Leu missense_variant 0.14
ccsA 619771 c.-120C>A upstream_gene_variant 0.15
ccsA 620656 p.Gly256Ser missense_variant 0.18
rpoC 764497 p.Glu376Asp missense_variant 0.33
rpoC 764571 p.Ser401Leu missense_variant 0.22
rpoC 764590 p.Lys407Asn missense_variant 0.18
rpoC 764633 p.Val422Phe missense_variant 0.14
rpoC 764747 p.Leu460Met missense_variant 0.12
rpoC 766535 p.Glu1056* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775881 p.Asn867Ile missense_variant 0.2
mmpL5 775981 p.Leu834Met missense_variant 0.13
mmpL5 776047 c.2434C>T synonymous_variant 0.13
mmpL5 776055 p.Val809Ala missense_variant 0.13
mmpL5 776060 c.2421C>G synonymous_variant 0.17
mmpL5 777841 p.Val214Met missense_variant 0.13
mmpL5 777905 c.576G>T synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303125 c.195G>T synonymous_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303987 p.Asp353Asn missense_variant 0.22
Rv1258c 1406553 p.Ala263Val missense_variant 0.29
atpE 1461163 p.Ala40Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474878 n.1221C>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
inhA 1674425 p.Ala75Asp missense_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103012 p.Pro11Ser missense_variant 0.12
PPE35 2168224 p.Pro797Ser missense_variant 0.18
PPE35 2168259 p.Thr785Met missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169308 c.1305C>T synonymous_variant 0.2
PPE35 2169397 p.Gly406Ser missense_variant 0.13
PPE35 2169457 p.His386Asp missense_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170220 c.393C>G synonymous_variant 0.16
PPE35 2170223 c.390T>C synonymous_variant 0.16
PPE35 2170238 c.375T>G synonymous_variant 0.15
Rv1979c 2221994 p.Ile391Val missense_variant 0.11
Rv1979c 2222021 p.Arg382* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289965 c.-724C>A upstream_gene_variant 0.14
kasA 2518609 p.Met165Ile missense_variant 0.22
kasA 2518612 c.498C>G synonymous_variant 0.22
kasA 2518902 p.Ala263Asp missense_variant 0.14
kasA 2519040 p.Asn309Ser missense_variant 0.17
folC 2747050 c.549C>A synonymous_variant 0.14
pepQ 2860601 c.-183C>A upstream_gene_variant 0.17
Rv2752c 3065155 p.Glu346Gly missense_variant 0.12
thyX 3068002 c.-57C>G upstream_gene_variant 0.12
thyA 3074051 p.Met141Val missense_variant 0.13
thyA 3074293 p.Leu60Gln missense_variant 0.17
thyA 3074582 c.-111T>C upstream_gene_variant 0.12
fbiD 3339586 p.Ala157Thr missense_variant 0.18
fprA 3474958 p.Val318Phe missense_variant 0.12
Rv3236c 3612199 c.918G>A synonymous_variant 0.17
Rv3236c 3612602 p.Leu172His missense_variant 0.18
Rv3236c 3612973 c.144C>A synonymous_variant 0.22
Rv3236c 3613098 p.Leu7Val missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878115 c.392delA frameshift_variant 0.2
rpoA 3878188 p.Ala107Asp missense_variant 0.17
ddn 3986867 c.24T>C synonymous_variant 0.12
embC 4240409 p.Pro183Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243047 p.Arg1062Gln missense_variant 0.17
embA 4243066 c.-167C>T upstream_gene_variant 0.15
embC 4243067 p.Asp1069Tyr missense_variant 0.15
embA 4244951 p.Gln573His missense_variant 0.14
embA 4246486 p.Gly1085Val missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.36
aftB 4267007 c.1830G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0