TB-Profiler result

Run: ERR2229313
Summary

Run ID: ERR2229313

Sample name:

Date: 31-03-2023 17:00:05

Number of reads: 809763

Percentage reads mapped: 96.33

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 5899 p.Asp220Glu missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7658 c.357A>T synonymous_variant 0.14
gyrA 7767 p.Tyr156Asn missense_variant 0.2
gyrA 9014 c.1713C>A synonymous_variant 0.21
fgd1 491067 p.Cys95* stop_gained 0.67
ccsA 619924 p.Arg12Ser missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.18
rpoB 762396 p.Arg864Ser missense_variant 0.25
rpoC 762947 c.-423C>T upstream_gene_variant 0.18
rpoC 764685 p.His439Arg missense_variant 0.18
rpoC 765133 c.1764G>T synonymous_variant 0.17
rpoC 765281 p.Thr638Pro missense_variant 0.29
rpoC 765677 p.Arg770Cys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776037 p.Ser815* stop_gained 0.2
mmpL5 776709 p.Cys591Phe missense_variant 0.5
mmpL5 776983 p.Leu500Met missense_variant 0.25
mmpL5 778086 c.394delG frameshift_variant 0.22
mmpR5 779079 p.Arg30Ser missense_variant 0.17
mmpS5 779650 c.-745A>G upstream_gene_variant 0.29
rpsL 781368 c.-192T>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406536 p.Gly269Ser missense_variant 0.17
Rv1258c 1407029 c.312G>T synonymous_variant 0.13
Rv1258c 1407059 p.Trp94Cys missense_variant 0.12
Rv1258c 1407112 p.Val77Met missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472931 n.1086T>C non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474170 n.513G>T non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
inhA 1674803 p.Ala201Val missense_variant 0.25
inhA 1674901 p.Asp234Tyr missense_variant 0.22
rpsA 1833384 c.-158C>T upstream_gene_variant 0.2
rpsA 1833412 c.-130C>A upstream_gene_variant 0.17
rpsA 1833933 c.393delC frameshift_variant 0.22
rpsA 1834580 p.Lys347Glu missense_variant 0.17
rpsA 1834705 c.1164C>A synonymous_variant 0.18
rpsA 1834956 p.Ala472Val missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102349 p.Ala232Thr missense_variant 0.4
katG 2155598 p.Ala172Ser missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.22
PPE35 2167868 c.2745A>C synonymous_variant 0.22
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2168220 p.Ala798Glu missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169293 c.1320T>C synonymous_variant 0.15
PPE35 2169570 p.Ser348Asn missense_variant 0.14
PPE35 2169573 p.Phe347Tyr missense_variant 0.14
PPE35 2169578 c.1035T>C synonymous_variant 0.14
PPE35 2169743 c.870G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170147 p.Ser156Ala missense_variant 0.13
PPE35 2170298 c.315A>G synonymous_variant 0.16
Rv1979c 2222086 p.Ala360Val missense_variant 0.18
Rv1979c 2222337 c.828G>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289275 c.-34T>A upstream_gene_variant 0.18
pncA 2290089 c.-848G>A upstream_gene_variant 0.29
ahpC 2726056 c.-137G>A upstream_gene_variant 0.17
ahpC 2726655 p.Gly155* stop_gained 0.15
folC 2746273 c.1326T>C synonymous_variant 0.17
folC 2746872 p.Glu243* stop_gained 0.22
ribD 2987326 p.Ile163Ser missense_variant 0.18
Rv2752c 3065651 p.Arg181Ser missense_variant 0.17
thyA 3073790 p.Pro228Thr missense_variant 0.12
ald 3087138 c.319T>C synonymous_variant 0.14
fbiB 3641726 c.192C>G synonymous_variant 0.12
alr 3841498 c.-78A>G upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.27
rpoA 3877529 c.978delC frameshift_variant 0.14
clpC1 4039508 c.1197G>C synonymous_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.22
clpC1 4039530 p.Asp392Ala missense_variant 0.22
clpC1 4039533 p.Asn391Thr missense_variant 0.22
clpC1 4039538 c.1167C>T synonymous_variant 0.22
clpC1 4039541 c.1164C>G synonymous_variant 0.22
clpC1 4039548 p.Ala386Ser missense_variant 0.29
clpC1 4039552 c.1153C>T synonymous_variant 0.22
clpC1 4039553 c.1152C>T synonymous_variant 0.25
clpC1 4039556 c.1149G>C synonymous_variant 0.2
clpC1 4039559 c.1146C>T synonymous_variant 0.22
clpC1 4039562 c.1143C>A synonymous_variant 0.17
clpC1 4039570 p.Met379Leu missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.21
embC 4240045 c.187delC frameshift_variant 0.18
embC 4240835 p.Gly325Cys missense_variant 0.22
embC 4240843 c.981C>T synonymous_variant 0.17
embC 4240847 p.Asp329Asn missense_variant 0.17
embC 4240862 p.Trp334Met missense_variant 0.18
embC 4240865 p.Ala335Thr missense_variant 0.18
embC 4241828 p.Lys656Glu missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243847 c.615C>A synonymous_variant 0.2
embA 4244381 c.1149G>T synonymous_variant 0.29
embA 4244590 c.1360delG frameshift_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.41
embB 4246548 p.Pro12Gln missense_variant 0.73
embB 4246555 c.42G>C synonymous_variant 0.86
embB 4246556 p.Ala15Pro missense_variant 0.86
aftB 4267231 p.Trp536Arg missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
ethA 4327689 c.-216G>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0