TB-Profiler result

Run: ERR2229548
Summary

Run ID: ERR2229548

Sample name:

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

Number of reads: 892948

Percentage reads mapped: 99.38

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 7207 c.-95C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576482 p.Val379Leu missense_variant 0.23
mshA 576616 c.1269G>T synonymous_variant 0.13
ccsA 619776 c.-115A>G upstream_gene_variant 0.12
rpoB 761198 c.1392G>A synonymous_variant 0.13
rpoC 765575 p.Val736Met missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775778 c.2703C>A synonymous_variant 0.25
mmpL5 776577 p.Thr635Asn missense_variant 0.14
mmpL5 776729 c.1752C>T synonymous_variant 0.15
mmpL5 777816 p.Val222Asp missense_variant 0.12
mmpR5 779062 p.Gly25Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800640 c.-169A>G upstream_gene_variant 0.1
fbiC 1303400 p.Gln157Arg missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416536 p.Ala271Val missense_variant 0.12
atpE 1460899 c.-146T>G upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472003 n.158A>T non_coding_transcript_exon_variant 0.12
rrs 1473064 n.1219A>T non_coding_transcript_exon_variant 0.13
rrl 1473793 n.136G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474573 n.916C>T non_coding_transcript_exon_variant 0.12
rrl 1476304 n.2647G>T non_coding_transcript_exon_variant 0.12
fabG1 1673152 c.-288A>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
fabG1 1674154 p.Val239Phe missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102192 p.Arg284Leu missense_variant 0.13
katG 2154550 p.Leu521Pro missense_variant 0.11
katG 2155644 c.468C>A synonymous_variant 0.2
PPE35 2167732 p.Phe961Ile missense_variant 0.18
PPE35 2167745 p.Thr956Arg missense_variant 0.19
PPE35 2167814 c.2799C>T synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168882 c.1731T>A synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.48
Rv1979c 2223239 c.-75G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714500 p.Leu278Pro missense_variant 0.12
folC 2746669 p.Glu310Asp missense_variant 0.15
ribD 2986845 p.Asp3His missense_variant 0.11
ribD 2986993 p.Gly52Val missense_variant 0.17
ribD 2987438 c.600G>T synonymous_variant 0.12
ribD 2987562 p.His242Asn missense_variant 0.13
Rv2752c 3065610 c.582C>A synonymous_variant 0.14
Rv2752c 3066073 p.Leu40Pro missense_variant 0.12
Rv2752c 3066284 c.-94delC upstream_gene_variant 0.17
thyX 3067585 p.Gly121Cys missense_variant 0.12
fprA 3474713 p.Glu236Gly missense_variant 0.22
fprA 3474779 p.Arg258His missense_variant 0.2
Rv3236c 3612018 p.Pro367Thr missense_variant 0.12
fbiB 3642030 p.Gly166Ser missense_variant 0.12
fbiB 3642194 p.Phe220Leu missense_variant 0.22
fbiB 3642622 p.Ala363Val missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3877572 c.936G>T synonymous_variant 0.12
clpC1 4038966 p.Ile580Thr missense_variant 0.17
clpC1 4039352 c.1353C>A synonymous_variant 0.14
clpC1 4040314 p.Leu131Met missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245682 p.Gly817Val missense_variant 0.14
embB 4246340 c.-174G>T upstream_gene_variant 0.15
embA 4246512 p.Pro1094Thr missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246794 p.Ala94Glu missense_variant 0.14
embB 4247592 p.Val360Ala missense_variant 0.12
embB 4248328 c.1815G>C synonymous_variant 0.19
aftB 4268873 c.-37C>A upstream_gene_variant 0.15
aftB 4269063 c.-227C>T upstream_gene_variant 0.12
ethR 4327030 c.-519C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407554 p.Arg217Trp missense_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0