TB-Profiler result

Run: ERR1949952
Summary

Run ID: ERR1949952

Sample name:

Date: 31-03-2023 15:35:31

Number of reads: 420817

Percentage reads mapped: 99.34

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
gyrB 5243 p.Ala2Ser missense_variant 0.25
gyrA 6634 c.-668T>A upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7480 p.Phe60Ser missense_variant 0.25
gyrA 8978 p.Phe559Leu missense_variant 0.4
gyrA 9035 c.1734G>T synonymous_variant 0.25
mshA 575964 p.Val206Gly missense_variant 0.5
mshA 576147 p.Val267Gly missense_variant 0.25
ccsA 619817 c.-74C>T upstream_gene_variant 0.2
ccsA 620068 p.Thr60Pro missense_variant 0.22
ccsA 620160 c.270A>G synonymous_variant 0.29
ccsA 620739 c.849A>T synonymous_variant 0.29
rpoB 759689 c.-118A>T upstream_gene_variant 0.4
rpoB 759732 c.-75C>A upstream_gene_variant 0.4
rpoB 759812 c.6A>T synonymous_variant 0.5
rpoB 760905 p.Phe367Ile missense_variant 0.3
rpoB 762316 p.Glu837Gly missense_variant 0.25
rpoB 762344 c.2542delT frameshift_variant 0.25
rpoC 765583 c.2214G>A synonymous_variant 0.2
rpoC 766120 p.Glu917Asp missense_variant 0.18
rpoC 766614 p.Lys1082Met missense_variant 0.25
rpoC 767106 p.Asn1246Ser missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.38
mmpL5 776003 c.2478C>T synonymous_variant 0.4
mmpL5 776008 p.His825Asp missense_variant 0.4
mmpL5 776009 c.2472A>G synonymous_variant 0.4
mmpL5 778078 p.Thr135Pro missense_variant 0.38
mmpR5 779038 p.Met17Leu missense_variant 0.4
mmpR5 779288 p.Phe100Tyr missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303766 p.Lys279Met missense_variant 0.33
fbiC 1303945 p.Ser339Pro missense_variant 0.5
fbiC 1304054 p.Asp375Gly missense_variant 0.29
Rv1258c 1406719 p.Leu208Val missense_variant 0.29
Rv1258c 1406914 p.Asn143Tyr missense_variant 0.2
Rv1258c 1407506 c.-166T>G upstream_gene_variant 0.4
embR 1416653 p.Lys232Met missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.56
rrs 1472217 n.372A>G non_coding_transcript_exon_variant 0.2
rrs 1472241 n.396A>C non_coding_transcript_exon_variant 0.43
rrs 1472698 n.853A>C non_coding_transcript_exon_variant 0.25
rrs 1472820 n.975T>A non_coding_transcript_exon_variant 0.29
rrs 1472853 n.1008A>T non_coding_transcript_exon_variant 0.33
rrl 1473954 n.297A>T non_coding_transcript_exon_variant 0.67
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475606 n.1949T>A non_coding_transcript_exon_variant 0.29
rrl 1476553 n.2896C>A non_coding_transcript_exon_variant 0.4
rpsA 1834162 p.Gln207His missense_variant 0.18
tlyA 1917769 c.-171C>T upstream_gene_variant 0.18
tlyA 1917951 c.12T>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918429 p.Leu164Val missense_variant 0.2
ndh 2102199 p.Ala282Thr missense_variant 0.33
ndh 2102573 p.Gln157Leu missense_variant 0.5
ndh 2102789 p.Leu85Pro missense_variant 0.25
ndh 2103176 c.-134G>C upstream_gene_variant 0.29
katG 2153998 p.Arg705Gln missense_variant 0.25
katG 2154979 p.Leu378Gln missense_variant 0.29
katG 2155017 c.1095G>C synonymous_variant 0.25
katG 2156075 p.Thr13Pro missense_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169298 p.Asn439Tyr missense_variant 0.4
PPE35 2169629 p.Asn328Lys missense_variant 0.75
PPE35 2170029 p.Met195Arg missense_variant 0.33
PPE35 2170035 p.Val193Gly missense_variant 0.43
Rv1979c 2222004 c.1161C>A synonymous_variant 0.25
Rv1979c 2222083 p.Leu361Arg missense_variant 0.75
Rv1979c 2222588 p.Tyr193Asn missense_variant 0.33
Rv1979c 2222991 c.174G>T synonymous_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289905 c.-664T>A upstream_gene_variant 0.67
pncA 2289927 c.-686T>A upstream_gene_variant 1.0
kasA 2518610 p.Thr166Pro missense_variant 0.2
kasA 2519199 p.Leu362Pro missense_variant 0.5
eis 2714398 p.His312Leu missense_variant 0.33
eis 2715154 p.Gly60Val missense_variant 0.22
eis 2715159 c.174G>T synonymous_variant 0.25
eis 2715240 p.Glu31Asp missense_variant 0.2
folC 2746226 p.Gly458Glu missense_variant 0.29
folC 2747085 p.Val172Met missense_variant 0.5
folC 2747403 p.Ser66Ala missense_variant 0.2
ribD 2986908 p.Thr24Pro missense_variant 0.18
ribD 2987238 p.Thr134Pro missense_variant 0.33
Rv2752c 3064903 p.Asp430Ala missense_variant 0.67
Rv2752c 3065954 p.Thr80Pro missense_variant 0.5
Rv2752c 3066355 c.-164T>G upstream_gene_variant 0.36
thyX 3067258 p.Phe230Ile missense_variant 0.33
thyX 3067390 p.Thr186Pro missense_variant 0.33
thyX 3067551 p.Leu132Gln missense_variant 0.6
thyX 3067974 c.-29T>A upstream_gene_variant 0.67
thyA 3073783 p.Leu230Gln missense_variant 0.4
ald 3087500 c.681T>G synonymous_variant 0.29
fprA 3474238 p.Phe78Val missense_variant 0.67
fprA 3475310 p.Glu435Ala missense_variant 0.17
whiB7 3568424 p.Pro86Thr missense_variant 0.22
whiB7 3568540 p.Pro47Gln missense_variant 0.29
fbiA 3641264 p.Val241Gly missense_variant 0.4
alr 3840536 p.Tyr295* stop_gained 0.33
alr 3841509 c.-89A>T upstream_gene_variant 0.5
rpoA 3877623 c.885C>T synonymous_variant 0.18
clpC1 4039018 p.Ser563Ala missense_variant 0.11
clpC1 4039022 c.1683A>G synonymous_variant 0.11
clpC1 4040691 p.Phe5Tyr missense_variant 0.2
embC 4240714 p.Trp284* stop_gained 0.2
embC 4241288 p.Ile476Leu missense_variant 0.25
embC 4242170 p.Thr770Pro missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242798 p.Asp979Gly missense_variant 0.25
embA 4242928 c.-305A>C upstream_gene_variant 0.4
embA 4243441 p.Leu70Arg missense_variant 0.25
embA 4243548 p.Phe106Val missense_variant 0.18
embA 4244748 p.Thr506Ser missense_variant 0.4
embA 4245835 p.Leu868Gln missense_variant 0.29
embA 4245873 p.Lys881* stop_gained 0.33
embA 4246333 p.Gln1034Pro missense_variant 0.22
embB 4246579 c.66T>G synonymous_variant 0.4
embB 4247039 p.Phe176Val missense_variant 0.4
embB 4248540 p.Phe676Cys missense_variant 0.3
embB 4248924 p.Met804Lys missense_variant 0.25
embB 4248998 p.Ser829Pro missense_variant 0.25
embB 4249313 p.Phe934Val missense_variant 0.25
aftB 4267343 c.1494C>A synonymous_variant 0.33
aftB 4268647 p.Thr64Ser missense_variant 0.29
aftB 4268799 p.Val13Gly missense_variant 0.29
aftB 4268903 c.-67A>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407736 p.Asn156Thr missense_variant 0.22
gid 4408444 c.-242A>C upstream_gene_variant 0.4
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0