TB-Profiler result

Run: ERR2229745
Summary

Run ID: ERR2229745

Sample name:

Date: 31-03-2023 17:32:22

Number of reads: 712474

Percentage reads mapped: 99.0

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2154860 p.Arg418* stop_gained 0.33 isoniazid
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 6887 c.-415C>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8088 c.790delC frameshift_variant 0.25
fgd1 490963 p.Val61Ile missense_variant 0.18
fgd1 491010 c.228C>A synonymous_variant 0.18
mshA 575225 c.-123T>G upstream_gene_variant 0.15
mshA 575876 p.Ala177Thr missense_variant 0.2
mshA 576417 p.Leu357Arg missense_variant 0.18
mshA 576519 p.Ser391Phe missense_variant 0.2
ccsA 620613 c.723C>A synonymous_variant 0.4
rpoB 761170 p.Gly455Val missense_variant 0.4
rpoB 761255 c.1449T>G synonymous_variant 0.2
rpoC 763808 p.Glu147Gln missense_variant 0.14
rpoC 764122 c.753C>T synonymous_variant 0.22
rpoC 765754 c.2385C>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776673 p.Val603Ala missense_variant 0.22
mmpL5 776878 p.Gln535Lys missense_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 777136 p.Met449Leu missense_variant 0.33
mmpL5 777142 p.Val447Met missense_variant 0.33
mmpL5 777232 p.Asp417Tyr missense_variant 0.15
mmpL5 778464 p.Thr6Ile missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781786 p.Glu76Gly missense_variant 0.12
rplC 801062 p.Arg85Gln missense_variant 0.22
fbiC 1303264 p.Gly112Cys missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305359 p.Thr810Met missense_variant 0.17
embR 1416940 c.408C>A synonymous_variant 0.33
embR 1416974 p.Ala125Glu missense_variant 0.5
embR 1417290 p.Gln20Lys missense_variant 0.13
atpE 1461200 c.156G>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473951 n.294G>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475184 n.1527T>C non_coding_transcript_exon_variant 0.12
rrl 1475201 n.1544G>A non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
inhA 1674889 p.Trp230Arg missense_variant 0.18
rpsA 1834513 c.972C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917973 p.Val12Ile missense_variant 0.29
ndh 2101859 p.Ile395Asn missense_variant 0.18
ndh 2101894 c.1149T>A synonymous_variant 0.18
ndh 2102159 p.Val295Gly missense_variant 0.22
katG 2155642 p.Lys157Met missense_variant 0.29
katG 2156126 c.-15C>A upstream_gene_variant 0.12
PPE35 2167955 c.2658A>C synonymous_variant 0.21
PPE35 2167965 p.Ala883Gly missense_variant 0.3
PPE35 2167967 c.2646A>C synonymous_variant 0.28
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168140 p.Ala825Thr missense_variant 0.29
PPE35 2168143 p.Phe824Leu missense_variant 0.29
PPE35 2168150 c.2463T>C synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.2
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.42
Rv1979c 2222333 p.Gly278* stop_gained 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289271 c.-30C>A upstream_gene_variant 0.14
kasA 2518161 p.Val16Ala missense_variant 0.14
kasA 2518864 c.750G>C synonymous_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.17
kasA 2518896 c.783_784delGT frameshift_variant 0.2
kasA 2519306 p.Val398Ile missense_variant 0.2
kasA 2519311 c.1197C>T synonymous_variant 0.18
eis 2714674 p.Pro220Leu missense_variant 0.18
folC 2746223 c.1374_1375delGG frameshift_variant 0.29
folC 2746839 p.Ala254Thr missense_variant 0.4
folC 2747533 c.66C>T synonymous_variant 0.12
pepQ 2859720 p.Met233Ile missense_variant 0.22
pepQ 2859725 p.Asp232Asn missense_variant 0.18
Rv2752c 3065305 p.Ala296Gly missense_variant 0.29
fprA 3474237 c.231C>G synonymous_variant 0.33
fbiB 3642660 p.Ala376Ser missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.32
clpC1 4039075 p.Arg544Ser missense_variant 0.15
clpC1 4039161 p.His515Gly missense_variant 0.2
clpC1 4039169 p.Glu512Asp missense_variant 0.19
clpC1 4039534 p.Asn391Asp missense_variant 0.15
clpC1 4039676 c.1029G>A synonymous_variant 0.33
clpC1 4039682 c.1023C>T synonymous_variant 0.33
clpC1 4039691 c.1014G>C synonymous_variant 0.22
embC 4241380 c.1518A>C synonymous_variant 0.13
embC 4241384 p.Pro508Ala missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243092 p.Leu1077Arg missense_variant 0.12
embC 4243095 p.Gly1078Val missense_variant 0.12
embA 4243099 c.-134G>C upstream_gene_variant 0.12
embA 4243102 c.-131G>T upstream_gene_variant 0.12
embC 4243103 p.Thr1081Pro missense_variant 0.12
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.12
embA 4243944 p.Thr238Pro missense_variant 0.2
embA 4244702 c.1470C>T synonymous_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.55
embB 4246556 p.Ala15Pro missense_variant 0.55
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.33
ethA 4326645 p.Asp277Tyr missense_variant 0.33
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 0.18
whiB6 4338571 c.-51delC upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0