TB-Profiler result

Run: ERR2229311
Summary

Run ID: ERR2229311

Sample name:

Date: 31-03-2023 17:00:17

Number of reads: 1142493

Percentage reads mapped: 98.83

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
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576519 p.Ser391Tyr missense_variant 0.33
rpoB 760359 p.Ile185Phe missense_variant 0.12
rpoB 760403 c.597C>A synonymous_variant 0.14
rpoB 760507 p.Ala234Glu missense_variant 0.17
rpoB 760972 p.Arg389Leu missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoC 764213 p.Arg282Gly missense_variant 0.4
rpoC 765428 p.Gln687Lys missense_variant 0.14
rpoC 766518 p.Thr1050Asn missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775653 p.Val943Asp missense_variant 0.15
mmpL5 775736 c.2745C>G synonymous_variant 0.14
mmpL5 775913 c.2568C>A synonymous_variant 0.4
mmpL5 776028 p.Leu818Pro missense_variant 0.14
mmpL5 776211 p.Tyr757Cys missense_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800825 p.Ile6Thr missense_variant 0.11
fbiC 1303533 p.Met201Ile missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407163 p.Leu60Met missense_variant 0.18
embR 1416774 p.Ala192Thr missense_variant 0.12
atpE 1461144 p.Ala34Lys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
inhA 1674438 c.237C>T synonymous_variant 0.2
rpsA 1834949 p.Leu470Met missense_variant 0.13
rpsA 1834978 c.1437C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154988 p.Pro375Gln missense_variant 0.12
katG 2155075 p.Ser346Ile missense_variant 0.18
PPE35 2167955 c.2658A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2167973 c.2640A>G synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169717 p.Asn299Ile missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.69
PPE35 2170053 p.Thr187Ser missense_variant 0.69
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289720 c.-479C>T upstream_gene_variant 0.25
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.24
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.12
kasA 2519167 c.1053T>C synonymous_variant 0.11
folC 2746619 p.Arg327Pro missense_variant 0.18
folC 2747538 p.Pro21Ala missense_variant 0.14
folC 2747662 c.-64G>A upstream_gene_variant 0.12
ribD 2986943 c.105G>A synonymous_variant 0.18
Rv2752c 3064648 p.Leu515Pro missense_variant 0.12
Rv2752c 3065875 p.Lys106Met missense_variant 0.25
thyA 3074559 c.-88C>A upstream_gene_variant 0.22
fprA 3474289 p.Glu95* stop_gained 0.13
whiB7 3568519 p.Ala54Asp missense_variant 0.14
Rv3236c 3612583 p.Trp178Cys missense_variant 0.3
Rv3236c 3612900 p.Leu73Met missense_variant 0.25
fbiA 3640500 c.-43A>G upstream_gene_variant 0.17
fbiB 3641885 p.Glu117Asp missense_variant 0.13
fbiB 3642829 p.Pro432Gln missense_variant 0.25
alr 3840300 p.Pro374His missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3878539 c.-32T>A upstream_gene_variant 0.33
clpC1 4038925 p.Leu594Ile missense_variant 0.13
clpC1 4039691 c.1014G>C synonymous_variant 0.13
clpC1 4039829 p.Leu292Phe missense_variant 0.11
clpC1 4039850 c.855T>C synonymous_variant 0.12
clpC1 4039858 p.Ile283Val missense_variant 0.14
panD 4044053 p.His77Asn missense_variant 0.15
panD 4044234 c.48C>T synonymous_variant 0.22
embC 4242198 p.Ala779Asp missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243815 p.Phe195Val missense_variant 0.17
embA 4244248 p.Val339Asp missense_variant 0.22
embA 4244292 p.Leu354Val missense_variant 0.2
embA 4245173 c.1941G>A synonymous_variant 0.17
embB 4245665 c.-849C>A upstream_gene_variant 0.25
embA 4246004 p.Asn924Lys missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.47
embB 4246556 p.Ala15Pro missense_variant 0.47
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.15
embB 4247022 c.510delG frameshift_variant 0.12
embB 4247028 p.Leu172Gln missense_variant 0.2
embB 4247033 p.Ser174Arg missense_variant 0.12
embB 4247066 p.Ile185Val missense_variant 0.12
embB 4247476 c.963C>A synonymous_variant 0.13
embB 4247851 c.1338C>A synonymous_variant 0.13
ethR 4327699 p.Ala51Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0