TB-Profiler result

Run: ERR2229633
Summary

Run ID: ERR2229633

Sample name:

Date: 31-03-2023 17:22:49

Number of reads: 796603

Percentage reads mapped: 99.09

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 6262 c.1023G>A synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7446 p.Lys49Glu missense_variant 0.13
gyrA 9078 p.Gly593Trp missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576588 p.Gly414Ala missense_variant 0.14
ccsA 620260 p.Ala124Ser missense_variant 0.13
rpoB 760284 p.Phe160Leu missense_variant 0.18
rpoC 764366 p.Gly333Ser missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775981 p.Leu834Met missense_variant 0.2
mmpL5 775987 p.His832Tyr missense_variant 0.2
mmpL5 775990 c.2491C>T synonymous_variant 0.2
mmpL5 776018 c.2463G>C synonymous_variant 0.22
mmpL5 776021 c.2460G>C synonymous_variant 0.22
mmpL5 776041 p.Ala814Thr missense_variant 0.25
mmpL5 776628 p.Asn618Ile missense_variant 0.24
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.16
mmpL5 777539 c.942T>A synonymous_variant 0.22
mmpR5 779302 p.Arg105Cys missense_variant 0.15
mmpR5 779322 p.Met111Ile missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800819 p.Lys4Arg missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304619 c.1689G>T synonymous_variant 0.14
Rv1258c 1406088 p.Ala418Val missense_variant 0.17
Rv1258c 1406768 c.573G>A synonymous_variant 0.13
embR 1416406 p.His314Gln missense_variant 0.12
embR 1416707 p.Ala214Asp missense_variant 0.13
embR 1416744 p.Pro202Thr missense_variant 0.14
atpE 1461005 c.-40G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.12
inhA 1674365 p.Pro55Leu missense_variant 0.25
rpsA 1833832 p.Glu97Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918361 p.Pro141Gln missense_variant 0.12
katG 2154016 p.Gly699Glu missense_variant 0.18
katG 2155302 p.His270Gln missense_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.3
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.38
PPE35 2167967 c.2646A>C synonymous_variant 0.41
PPE35 2167973 c.2640A>G synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169091 p.Val508Leu missense_variant 0.2
PPE35 2169269 c.1344A>G synonymous_variant 0.23
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169488 c.1125G>C synonymous_variant 0.28
PPE35 2169491 c.1122T>C synonymous_variant 0.28
PPE35 2169732 p.Asn294Ser missense_variant 0.15
PPE35 2169833 c.780A>C synonymous_variant 0.17
PPE35 2169838 p.Ile259Leu missense_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2222333 p.Gly278Arg missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289856 c.-615G>T upstream_gene_variant 0.18
kasA 2518649 p.Ala179Ser missense_variant 0.4
kasA 2519128 c.1014G>C synonymous_variant 0.21
kasA 2519131 c.1017G>C synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.15
eis 2714356 p.Gly326Val missense_variant 0.21
folC 2746303 c.1296C>A synonymous_variant 0.22
folC 2747419 c.180C>T synonymous_variant 0.17
pepQ 2859761 p.Ile220Val missense_variant 0.14
pepQ 2860028 c.391C>T synonymous_variant 0.13
Rv2752c 3065226 p.Glu322Asp missense_variant 0.25
Rv2752c 3065381 p.Arg271Ser missense_variant 0.29
ald 3087411 p.Asp198Asn missense_variant 0.17
fbiD 3339564 c.447G>C synonymous_variant 0.12
fbiD 3339750 c.633C>T synonymous_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.18
whiB7 3568486 p.Val65Gly missense_variant 0.15
fbiB 3641373 c.-162C>A upstream_gene_variant 0.15
fbiB 3641637 p.Ala35Thr missense_variant 0.2
alr 3840555 p.Ala289Glu missense_variant 0.13
alr 3840834 p.His196Leu missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.26
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.27
embC 4240996 c.1134G>A synonymous_variant 0.12
embC 4241446 c.1584C>T synonymous_variant 0.13
embC 4241528 p.Arg556Cys missense_variant 0.17
embC 4241852 p.Ala664Ser missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245563 c.-951G>T upstream_gene_variant 0.18
embB 4246553 p.Arg14Gly missense_variant 0.25
embB 4247200 c.687C>G synonymous_variant 0.12
embB 4247201 p.Val230Ile missense_variant 0.12
embB 4248481 c.1970delA frameshift_variant 0.12
aftB 4267020 p.Pro606Leu missense_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0