TB-Profiler result

Run: ERR2229176
Summary

Run ID: ERR2229176

Sample name:

Date: 31-03-2023 16:46:42

Number of reads: 707576

Percentage reads mapped: 99.14

Strain: lineage4

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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7646 c.347delT frameshift_variant 0.25
gyrA 7895 c.594C>T synonymous_variant 0.12
gyrA 9755 c.2454C>T synonymous_variant 0.12
mshA 575893 c.546C>T synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620278 p.Arg130Cys missense_variant 0.29
ccsA 620341 p.Val151Leu missense_variant 0.15
rpoB 759709 c.-98C>T upstream_gene_variant 0.14
rpoB 761015 c.1209G>C synonymous_variant 0.12
rpoB 761027 c.1221A>C synonymous_variant 0.11
rpoB 761036 c.1230G>C synonymous_variant 0.11
rpoB 761037 c.1231T>C synonymous_variant 0.11
rpoB 762556 p.Pro917Gln missense_variant 0.15
mmpL5 775629 p.Pro951Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 0.94
mmpL5 775741 c.2740C>T synonymous_variant 0.15
mmpL5 775814 c.2667C>G synonymous_variant 0.15
mmpL5 775817 c.2664T>C synonymous_variant 0.15
mmpL5 775820 c.2661G>A synonymous_variant 0.15
mmpL5 776048 c.2433G>A synonymous_variant 0.18
mmpR5 779038 p.Met17Leu missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303276 p.Ala116Ser missense_variant 0.12
fbiC 1303512 c.582T>C synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304676 c.1746A>C synonymous_variant 0.12
fbiC 1304679 p.Glu583Asp missense_variant 0.12
fbiC 1304680 p.Val584Leu missense_variant 0.13
fbiC 1304683 p.Ala585Ser missense_variant 0.13
fbiC 1305210 c.2283delC frameshift_variant 0.11
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.14
Rv1258c 1406946 p.Ala132Gly missense_variant 0.14
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.14
embR 1416874 c.473delT frameshift_variant 0.14
embR 1416978 p.His124Asn missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 0.96
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474566 n.912delA non_coding_transcript_exon_variant 0.14
rrl 1476236 n.2579G>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
inhA 1673523 c.-679G>T upstream_gene_variant 0.2
rpsA 1833995 p.Leu152Met missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918231 p.Glu98Lys missense_variant 0.17
ndh 2101828 c.1215C>A synonymous_variant 0.12
ndh 2102877 p.Tyr56Asn missense_variant 0.29
katG 2155244 p.Ala290Ser missense_variant 0.13
katG 2155946 p.Asp56Tyr missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.31
PPE35 2169910 p.Asn235Tyr missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289933 c.-692G>T upstream_gene_variant 0.33
kasA 2518220 p.Leu36Met missense_variant 0.14
kasA 2518798 c.684G>C synonymous_variant 0.2
kasA 2518801 c.687G>A synonymous_variant 0.2
kasA 2518809 p.Lys232Arg missense_variant 0.18
kasA 2519287 c.1173T>C synonymous_variant 0.14
folC 2747401 c.198G>T synonymous_variant 0.17
pepQ 2859448 p.Val324Thr missense_variant 0.13
pepQ 2859453 c.966G>C synonymous_variant 0.14
pepQ 2859457 p.Val321Thr missense_variant 0.14
Rv2752c 3064997 p.Thr399Ala missense_variant 0.14
Rv2752c 3065283 c.909C>A synonymous_variant 0.12
Rv2752c 3065576 p.Ala206Ser missense_variant 0.22
thyX 3067372 p.Trp192Arg missense_variant 0.29
thyX 3067376 c.570G>A synonymous_variant 0.25
thyX 3067618 p.Pro110Thr missense_variant 0.14
thyA 3074244 c.228A>G synonymous_variant 0.14
Rv3083 3448325 c.-179G>T upstream_gene_variant 0.13
fprA 3474292 p.Arg96Ser missense_variant 0.14
whiB7 3568646 p.Arg12* stop_gained 0.14
whiB7 3568654 p.Gln9Arg missense_variant 0.13
Rv3236c 3612931 c.186G>T synonymous_variant 0.25
Rv3236c 3613018 c.99T>C synonymous_variant 0.13
fbiA 3640403 c.-140G>A upstream_gene_variant 0.15
fbiA 3640430 c.-113A>T upstream_gene_variant 0.18
fbiB 3641193 c.-342G>T upstream_gene_variant 0.15
fbiB 3642169 p.Thr212Lys missense_variant 0.22
alr 3840506 c.915C>A synonymous_variant 0.14
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
ddn 3986800 c.-44C>T upstream_gene_variant 0.22
clpC1 4039355 c.1350G>A synonymous_variant 0.15
clpC1 4039728 p.Asp326Gly missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.12
embC 4239863 c.1A>C initiator_codon_variant 0.14
embC 4242175 c.2313G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243901 c.669G>T synonymous_variant 0.22
embA 4245365 p.Phe711Leu missense_variant 0.14
embB 4247028 p.Leu172Arg missense_variant 0.43
aftB 4267225 p.Ile538Phe missense_variant 0.14
aftB 4268493 p.Ala115Glu missense_variant 0.18
aftB 4268731 p.Arg36Trp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448494 c.-9_*1408del transcript_ablation 1.0