TB-Profiler result

Run: ERR2513173
Summary

Run ID: ERR2513173

Sample name:

Date: 31-03-2023 19:30:10

Number of reads: 491685

Percentage reads mapped: 99.66

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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 5641 c.402G>A synonymous_variant 0.25
gyrB 6149 p.Phe304Leu missense_variant 0.13
gyrB 6158 c.921delC frameshift_variant 0.12
gyrB 6333 p.Pro365Arg missense_variant 0.17
gyrA 6769 c.-533C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7587 p.Leu96Met missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490864 p.Glu28Lys missense_variant 0.2
fgd1 490896 p.Ser38Arg missense_variant 0.12
fgd1 491047 p.Ala89Thr missense_variant 0.29
fgd1 491218 p.Asp146Tyr missense_variant 0.29
ccsA 620130 c.240G>A synonymous_variant 0.33
rpoB 759756 c.-51C>T upstream_gene_variant 0.14
rpoB 760306 p.Arg167His missense_variant 0.22
rpoB 760499 c.693G>A synonymous_variant 0.13
rpoB 760563 p.Arg253* stop_gained 0.25
rpoB 761281 p.Gly492Asp missense_variant 0.12
rpoB 761349 p.Asp515His missense_variant 0.14
rpoB 761807 c.2001C>T synonymous_variant 0.22
rpoB 762744 p.Gln980* stop_gained 0.29
rpoB 762833 p.Ser1009Arg missense_variant 0.17
rpoC 763265 c.-105G>A upstream_gene_variant 0.15
rpoB 763321 p.Ala1172Glu missense_variant 0.12
rpoC 763891 c.522G>A synonymous_variant 0.22
rpoC 764332 c.963G>A synonymous_variant 0.2
rpoC 764625 p.Gly419Asp missense_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765784 c.2415C>G synonymous_variant 0.1
rpoC 765793 c.2424C>G synonymous_variant 0.1
rpoC 765811 c.2442T>C synonymous_variant 0.12
rpoC 765814 c.2445A>G synonymous_variant 0.12
rpoC 765886 c.2517C>G synonymous_variant 0.1
rpoC 765892 c.2523T>C synonymous_variant 0.11
rpoC 765925 p.Asn852Lys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776199 p.Thr761Asn missense_variant 0.22
mmpL5 776345 c.2136C>T synonymous_variant 0.11
mmpL5 776391 p.Asp697Gly missense_variant 0.13
mmpL5 777711 p.Gly257Glu missense_variant 0.13
mmpL5 778489 c.-9G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781472 c.-88G>T upstream_gene_variant 0.15
rplC 800617 c.-192C>T upstream_gene_variant 0.11
rplC 801072 c.264C>T synonymous_variant 0.13
rplC 801257 p.Ser150Tyr missense_variant 0.14
rplC 801399 c.591G>A synonymous_variant 0.13
fbiC 1304490 c.1560C>A synonymous_variant 0.13
fbiC 1304500 p.Ala524Thr missense_variant 0.13
embR 1416630 p.Gly240Cys missense_variant 0.12
embR 1417140 p.Ala70Ser missense_variant 1.0
atpE 1460916 c.-129G>A upstream_gene_variant 0.15
atpE 1461000 c.-45C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472059 n.214T>C non_coding_transcript_exon_variant 0.29
rrs 1473353 n.1508C>T non_coding_transcript_exon_variant 0.15
rrl 1475178 n.1521T>C non_coding_transcript_exon_variant 0.12
rrl 1475945 n.2288C>T non_coding_transcript_exon_variant 0.22
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.14
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
inhA 1674187 c.-15A>G upstream_gene_variant 0.17
inhA 1674190 c.-12A>G upstream_gene_variant 0.17
inhA 1674888 c.687C>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102655 p.His130Asn missense_variant 0.15
ndh 2103032 c.10delC frameshift_variant 0.5
katG 2154215 p.Val633Ile missense_variant 0.29
katG 2154916 p.Glu399Ala missense_variant 0.18
katG 2155096 p.Tyr339Cys missense_variant 0.17
katG 2155577 p.Lys179Glu missense_variant 0.2
katG 2155662 c.450G>A synonymous_variant 0.2
PPE35 2167745 p.Thr956Arg missense_variant 0.11
Rv1979c 2221741 p.Gly475Val missense_variant 0.13
Rv1979c 2222924 p.Tyr81His missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289738 c.-497G>A upstream_gene_variant 0.15
kasA 2518385 p.Gly91Cys missense_variant 0.14
kasA 2518981 p.Arg289Ser missense_variant 0.18
eis 2715013 p.Arg107His missense_variant 0.5
eis 2715273 c.60C>T synonymous_variant 0.13
ahpC 2726341 p.Val50Gly missense_variant 0.38
ahpC 2726693 c.501C>A synonymous_variant 0.12
folC 2746531 c.1068G>A synonymous_variant 0.18
folC 2746563 p.Pro346Ser missense_variant 0.15
folC 2746572 p.Arg343Ser missense_variant 0.22
folC 2747022 p.Val193Ile missense_variant 1.0
pepQ 2859579 c.840G>T synonymous_variant 0.12
pepQ 2859817 p.Ala201Val missense_variant 0.2
pepQ 2860264 p.Ala52Asp missense_variant 0.2
Rv2752c 3065020 p.Arg391His missense_variant 0.25
Rv2752c 3065315 p.Glu293Lys missense_variant 0.18
Rv2752c 3065616 c.576C>T synonymous_variant 0.15
Rv2752c 3065842 p.Arg117Leu missense_variant 0.11
Rv2752c 3065950 p.His81Leu missense_variant 0.22
Rv2752c 3066290 c.-99G>T upstream_gene_variant 0.11
thyA 3074645 c.-174T>G upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087332 c.513C>T synonymous_variant 0.12
fbiD 3339303 c.186C>A synonymous_variant 0.15
fbiD 3339659 p.Ala181Val missense_variant 0.17
fbiD 3339667 p.Gly184Ser missense_variant 0.17
Rv3083 3448536 c.33C>T synonymous_variant 0.29
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449379 c.876G>A synonymous_variant 0.12
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
Rv3083 3449673 c.1170C>T synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474179 p.Pro58Leu missense_variant 0.17
fprA 3474805 p.Met267Val missense_variant 0.14
fprA 3475327 c.1321C>A synonymous_variant 0.25
Rv3236c 3613250 c.-134G>A upstream_gene_variant 0.14
fbiA 3640616 p.Leu25Pro missense_variant 0.13
fbiA 3640913 p.Pro124Leu missense_variant 0.12
fbiA 3641164 p.Ile208Val missense_variant 1.0
fbiB 3641964 p.Val144Ile missense_variant 0.29
fbiB 3642055 p.Arg174His missense_variant 0.17
rpoA 3877821 c.687C>T synonymous_variant 0.2
ddn 3986691 c.-153G>A upstream_gene_variant 0.18
ddn 3986959 p.Gly39Asp missense_variant 0.12
clpC1 4038383 c.2322G>A synonymous_variant 0.25
clpC1 4039591 p.Val372Leu missense_variant 0.12
clpC1 4039792 p.Ala305Thr missense_variant 0.17
embC 4239666 c.-197C>T upstream_gene_variant 0.18
embC 4240136 p.Ala92Thr missense_variant 0.12
embC 4240557 p.Ala232Val missense_variant 0.12
embC 4240585 c.723C>T synonymous_variant 0.14
embC 4242137 p.Leu759Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244432 c.1200C>T synonymous_variant 0.22
embA 4245407 c.2175G>A synonymous_variant 0.5
embA 4245804 p.Gln858* stop_gained 0.18
embB 4246890 p.Thr126Asn missense_variant 0.29
embB 4247837 c.1324C>T synonymous_variant 0.18
embB 4248940 c.2427C>T synonymous_variant 0.14
embB 4249081 c.2568C>T synonymous_variant 0.2
embB 4249736 p.Pro1075Ser missense_variant 0.29
aftB 4267081 p.Arg586* stop_gained 0.12
aftB 4268581 p.Leu86Met missense_variant 0.18
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
aftB 4269027 c.-191C>T upstream_gene_variant 0.18
ubiA 4269912 c.-79T>C upstream_gene_variant 0.12
ethA 4326346 c.1128C>A synonymous_variant 0.11
whiB6 4338413 p.Asp37His missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338669 c.-148C>T upstream_gene_variant 0.13
gid 4407598 p.Val202Ala missense_variant 0.15