TB-Profiler result

Run: ERR2229156
Summary

Run ID: ERR2229156

Sample name:

Date: 31-03-2023 16:45:43

Number of reads: 825399

Percentage reads mapped: 99.13

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 8772 p.Gly491Ser missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.39
ccsA 620705 p.Trp272Leu missense_variant 0.13
rpoB 760390 p.Ser195Ile missense_variant 0.15
rpoB 760570 p.Thr255Lys missense_variant 0.18
rpoB 760724 c.918T>C synonymous_variant 0.13
rpoC 764214 p.Arg282Gln missense_variant 0.13
rpoC 765876 p.Val836Asp missense_variant 0.13
rpoC 766275 p.Ala969Gly missense_variant 0.11
rpoC 766278 c.2909_2910insACGT frameshift_variant 0.12
rpoC 766847 p.Gln1160Lys missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776526 p.Met652Thr missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303081 p.Arg51Cys missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406286 p.Met352Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472110 n.265G>T non_coding_transcript_exon_variant 0.12
rrs 1472199 n.354C>A non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
rpsA 1833697 c.156C>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.93
ndh 2102198 p.Ala282Val missense_variant 0.25
katG 2155699 p.Asn138Ile missense_variant 0.12
PPE35 2167833 p.Leu927Arg missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2167936 p.Thr893Ala missense_variant 0.11
PPE35 2167937 c.2676A>C synonymous_variant 0.11
PPE35 2168051 p.Val854Ile missense_variant 0.2
PPE35 2168059 p.Gln852Glu missense_variant 0.2
PPE35 2168140 p.Ala825Thr missense_variant 0.22
PPE35 2168143 p.Phe824Leu missense_variant 0.22
PPE35 2168150 c.2463T>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169287 c.1326T>C synonymous_variant 0.27
PPE35 2170038 p.Ala192Val missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.55
PPE35 2170066 p.Ala183Thr missense_variant 0.14
PPE35 2170540 c.73C>T synonymous_variant 0.17
PPE35 2170571 p.Leu14Phe missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289284 c.-43T>A upstream_gene_variant 0.15
pncA 2289356 c.-115G>T upstream_gene_variant 0.12
eis 2714459 p.Asp292Asn missense_variant 0.15
eis 2714687 p.Ala216Ser missense_variant 0.14
pepQ 2860141 p.Gly93Val missense_variant 0.13
ribD 2987371 p.Leu178Arg missense_variant 0.12
Rv2752c 3064559 p.Tyr545Asp missense_variant 0.14
Rv2752c 3064677 c.1515A>G synonymous_variant 0.14
Rv2752c 3065752 p.Asn147Ser missense_variant 0.22
thyX 3067536 p.Asp137Cys missense_variant 0.25
thyX 3068089 c.-144C>A upstream_gene_variant 0.12
thyA 3073968 c.504C>A synonymous_variant 0.15
ald 3087446 c.627C>A synonymous_variant 0.2
fprA 3473857 c.-150G>T upstream_gene_variant 0.18
fprA 3474356 p.Glu117Val missense_variant 0.2
fprA 3475031 p.Pro342His missense_variant 0.15
fprA 3475183 p.Ala393Ser missense_variant 0.15
fprA 3475330 p.Val442Leu missense_variant 0.18
fbiB 3640875 c.-660C>G upstream_gene_variant 0.14
fbiA 3641370 p.Tyr276* stop_gained 0.12
fbiA 3641524 c.984_985delAG frameshift_variant 0.12
alr 3840582 p.Ala280Asp missense_variant 0.13
alr 3841239 p.Leu61Pro missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4038858 p.Arg616His missense_variant 0.12
clpC1 4039508 c.1197G>C synonymous_variant 0.12
clpC1 4039526 c.1179G>C synonymous_variant 0.11
clpC1 4039530 p.Asp392Ala missense_variant 0.11
clpC1 4039548 p.Ala386Gly missense_variant 0.11
clpC1 4039552 c.1153C>T synonymous_variant 0.11
clpC1 4039556 c.1149G>C synonymous_variant 0.11
clpC1 4039562 c.1143C>A synonymous_variant 0.11
clpC1 4039645 p.His354Asp missense_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.14
panD 4044153 c.129G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244505 p.Gly425Trp missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246601 p.Ala30Thr missense_variant 0.25
embB 4247512 c.999T>C synonymous_variant 0.26
embB 4247516 p.Asn335Asp missense_variant 0.25
aftB 4267754 p.Lys361Asn missense_variant 0.2
aftB 4268017 p.Val274Leu missense_variant 0.2
aftB 4268197 p.Val214Leu missense_variant 0.12
ethA 4326767 p.Thr236Asn missense_variant 0.13
ethA 4327581 c.-108C>T upstream_gene_variant 0.12
whiB6 4338364 p.Cys53Phe missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0