TB-Profiler result

Run: ERR2229547
Summary

Run ID: ERR2229547

Sample name:

Date: 31-03-2023 17:18:40

Number of reads: 801592

Percentage reads mapped: 99.4

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9432 c.2131C>T synonymous_variant 0.12
fgd1 490828 p.Ala16Ser missense_variant 0.12
fgd1 491458 p.Asp226Tyr missense_variant 0.18
mshA 575371 p.Asp8Glu missense_variant 0.22
ccsA 620246 p.Leu119* stop_gained 0.12
rpoB 760500 p.Leu232Phe missense_variant 0.33
rpoB 761316 p.Gly504Arg missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801114 c.306C>T synonymous_variant 0.12
rplC 801185 p.Thr126Asn missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304852 p.Gly641Val missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472541 n.696T>C non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474836 n.1179A>C non_coding_transcript_exon_variant 0.29
rrl 1476471 n.2814G>A non_coding_transcript_exon_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
rpsA 1833391 c.-151G>T upstream_gene_variant 0.13
rpsA 1834294 c.753G>T synonymous_variant 0.17
rpsA 1834684 c.1143C>A synonymous_variant 0.13
rpsA 1834751 p.Leu404Ile missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918224 c.285G>T synonymous_variant 0.17
ndh 2102474 p.Ala190Asp missense_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.24
PPE35 2169879 p.Phe245Tyr missense_variant 0.15
PPE35 2169884 c.729T>C synonymous_variant 0.19
PPE35 2169897 p.Ser239Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.24
PPE35 2170518 p.Asp32Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290004 c.-763A>T upstream_gene_variant 0.14
kasA 2518882 c.768C>A synonymous_variant 0.12
eis 2714899 p.Arg145Leu missense_variant 0.25
folC 2746510 c.1089A>T synonymous_variant 0.25
Rv2752c 3064953 c.1239C>T synonymous_variant 0.14
Rv2752c 3065712 c.480C>T synonymous_variant 0.2
Rv2752c 3066287 c.-96G>A upstream_gene_variant 0.12
Rv2752c 3067157 c.-966G>T upstream_gene_variant 0.17
ald 3086877 p.Pro20Thr missense_variant 0.12
ald 3086935 p.Ala39Asp missense_variant 0.13
fprA 3474624 c.618G>T synonymous_variant 0.14
whiB7 3568830 c.-151T>C upstream_gene_variant 0.15
Rv3236c 3612869 p.Ala83Asp missense_variant 0.25
fbiA 3641538 c.996A>T stop_lost&splice_region_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877998 c.509dupC frameshift_variant 0.12
rpoA 3878627 c.-120T>G upstream_gene_variant 0.4
clpC1 4039161 p.His515Gly missense_variant 0.15
clpC1 4039530 p.Asp392Ala missense_variant 0.18
clpC1 4040458 p.Arg83Ser missense_variant 0.14
embC 4241206 c.1344G>T synonymous_variant 0.13
embC 4241364 p.Leu501Pro missense_variant 0.14
embA 4242511 c.-722G>C upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243479 p.Pro83Thr missense_variant 0.22
embA 4243505 c.273C>A synonymous_variant 0.13
embA 4244096 c.864C>A synonymous_variant 0.12
embA 4244943 p.Ala571Pro missense_variant 0.12
embA 4245407 c.2175G>A synonymous_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4247068 c.555T>C synonymous_variant 0.17
embB 4248282 p.Thr590Asn missense_variant 0.12
embB 4248814 c.2301G>C synonymous_variant 0.12
aftB 4267987 p.Arg284Cys missense_variant 0.14
aftB 4268439 p.Asp133Gly missense_variant 0.11
ubiA 4269478 p.Met119Lys missense_variant 0.13
ubiA 4269993 c.-160A>T upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
ethA 4327121 p.Val118Ala missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0