TB-Profiler result

Run: ERR2229363
Summary

Run ID: ERR2229363

Sample name:

Date: 31-03-2023 17:05:52

Number of reads: 1045709

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
fgd1 491382 p.Glu200Asp missense_variant 0.17
fgd1 491716 p.Ala312Thr missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620333 p.Leu148Gln missense_variant 0.12
rpoB 760423 p.Leu206Pro missense_variant 0.15
rpoB 762057 p.Ile751Val missense_variant 0.12
rpoB 762062 c.2256T>C synonymous_variant 0.13
rpoB 762065 c.2259T>C synonymous_variant 0.12
rpoB 762068 c.2262C>T synonymous_variant 0.12
rpoC 764116 c.747C>T synonymous_variant 0.17
rpoC 764787 p.Lys473Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.17
mmpL5 776021 c.2460G>C synonymous_variant 0.17
mmpS5 779509 c.-604G>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781538 c.-22G>T upstream_gene_variant 0.18
rpsL 781639 p.Ser27Ile missense_variant 0.13
rpsL 781666 p.Arg36Leu missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303945 p.Ser339Thr missense_variant 0.15
atpE 1461284 c.240C>T synonymous_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
rrl 1475119 n.1462C>A non_coding_transcript_exon_variant 0.14
rrl 1475140 n.1483T>C non_coding_transcript_exon_variant 0.18
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
inhA 1674292 p.Glu31* stop_gained 0.22
rpsA 1833978 p.Gly146Val missense_variant 0.12
rpsA 1834726 c.1185C>A synonymous_variant 0.12
rpsA 1834801 p.Glu420Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102292 p.Asp251Asn missense_variant 0.15
ndh 2102433 p.Ile204Val missense_variant 0.11
ndh 2102641 p.Phe134Leu missense_variant 0.12
ndh 2102964 p.Leu27Ile missense_variant 0.2
PPE35 2167781 c.2832C>A synonymous_variant 0.21
PPE35 2167814 c.2799C>T synonymous_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.11
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2168052 p.Val854Glu missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169725 c.888T>C synonymous_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.76
PPE35 2170053 p.Thr187Ser missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747193 p.Gln136* stop_gained 0.12
pepQ 2859927 c.492G>C synonymous_variant 0.17
ribD 2987364 p.Ala176Ser missense_variant 0.14
Rv2752c 3065496 c.696G>T synonymous_variant 0.13
thyX 3067471 p.Asn159Asp missense_variant 0.12
thyX 3067483 p.Ala155Ser missense_variant 0.15
thyX 3067714 p.Val78Leu missense_variant 0.13
thyA 3074174 p.Ser100Pro missense_variant 0.17
ald 3087392 c.573C>G synonymous_variant 0.13
ald 3087917 c.1098C>T synonymous_variant 0.14
fbiD 3339234 c.117G>T synonymous_variant 0.14
fbiD 3339473 p.Ala119Glu missense_variant 0.12
Rv3083 3448365 c.-139T>C upstream_gene_variant 0.14
fprA 3475032 c.1026C>A synonymous_variant 0.12
Rv3236c 3612150 p.Gln323* stop_gained 0.22
fbiA 3641067 c.526delT frameshift_variant 0.15
fbiB 3641699 p.Lys55Asn missense_variant 0.12
fbiB 3641964 p.Val144Ile missense_variant 0.15
alr 3840797 c.624C>T synonymous_variant 0.17
rpoA 3878318 p.Thr64Ala missense_variant 0.12
ddn 3986813 c.-31T>A upstream_gene_variant 0.12
clpC1 4038545 c.2160C>T synonymous_variant 0.12
clpC1 4039003 p.Asn568Asp missense_variant 0.13
clpC1 4039275 p.Ala477Glu missense_variant 0.11
clpC1 4039577 c.1128T>C synonymous_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4040457 c.247delC frameshift_variant 0.15
embC 4242295 p.Asp811Glu missense_variant 0.33
embC 4242410 p.Val850Met missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.14
embA 4244110 p.Tyr293Phe missense_variant 0.15
embA 4244631 p.Thr467Ala missense_variant 0.11
embA 4244989 p.Ala586Gly missense_variant 0.11
embA 4245271 p.Arg680Gln missense_variant 0.14
embB 4245803 c.-711C>T upstream_gene_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246553 p.Arg14Ser missense_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.75
embB 4247481 p.Phe323Ser missense_variant 0.11
ubiA 4269494 p.Leu114Met missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408208 c.-6T>C upstream_gene_variant 0.13