TB-Profiler result

Run: ERR2513638
Summary

Run ID: ERR2513638

Sample name:

Date: 31-03-2023 19:48:46

Number of reads: 3207492

Percentage reads mapped: 99.7

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 5210 c.-30C>A upstream_gene_variant 0.25
gyrB 6267 p.Pro343Leu missense_variant 0.13
gyrA 6604 c.-698G>A upstream_gene_variant 0.4
gyrA 6739 c.-563C>A upstream_gene_variant 0.33
gyrA 7022 c.-280C>T upstream_gene_variant 0.33
gyrB 7237 p.Asn666Lys missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7661 c.360C>T synonymous_variant 0.12
gyrA 8730 p.Gly477Trp missense_variant 0.2
gyrA 8917 p.Arg539His missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575887 c.540G>A synonymous_variant 0.4
mshA 576523 c.1176G>A synonymous_variant 0.29
ccsA 620106 c.216C>T synonymous_variant 0.17
rpoB 759920 c.114G>T synonymous_variant 0.17
rpoB 760061 p.Tyr85* stop_gained 0.15
rpoB 761187 p.Arg461Cys missense_variant 0.67
rpoC 763157 c.-213G>T upstream_gene_variant 0.11
rpoC 763412 p.Ala15Ser missense_variant 0.29
rpoC 763635 p.Arg89His missense_variant 0.14
rpoC 764092 c.723C>T synonymous_variant 0.14
rpoC 765487 p.Met706Ile missense_variant 0.2
rpoC 767018 p.Thr1217Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775803 p.Met893Thr missense_variant 0.29
mmpL5 776072 c.2409C>T synonymous_variant 0.18
mmpL5 776136 p.Ser782Tyr missense_variant 0.17
mmpL5 776575 p.Ala636Ser missense_variant 0.14
mmpL5 776578 p.Thr635Ala missense_variant 0.14
mmpL5 777183 p.Ala433Val missense_variant 0.13
mmpL5 777376 p.Glu369Lys missense_variant 0.15
mmpL5 777445 p.Val346Phe missense_variant 0.13
mmpL5 777606 p.Gly292Val missense_variant 0.18
mmpL5 777932 p.Lys183Asn missense_variant 0.15
mmpL5 778023 p.Leu153His missense_variant 0.13
mmpL5 778098 p.Asp128Gly missense_variant 0.11
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 1.0
rplC 801302 p.Arg165Gln missense_variant 0.12
fbiC 1303064 p.Ala45Asp missense_variant 0.12
fbiC 1303363 p.Phe145Leu missense_variant 0.11
fbiC 1303564 p.Gly212Ser missense_variant 0.15
fbiC 1303919 p.Arg330His missense_variant 0.15
fbiC 1304987 p.Pro686Leu missense_variant 0.12
fbiC 1305357 c.2427C>G synonymous_variant 0.11
Rv1258c 1406186 c.1155G>A synonymous_variant 0.33
Rv1258c 1406811 p.Thr177Ile missense_variant 0.12
Rv1258c 1407505 c.-165G>A upstream_gene_variant 0.2
embR 1416621 p.Pro243Ser missense_variant 0.12
embR 1416674 p.Leu225Pro missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471675 n.-171G>T upstream_gene_variant 0.17
inhA 1673934 c.-268C>T upstream_gene_variant 0.14
inhA 1674545 p.Asp115Gly missense_variant 0.29
inhA 1674793 p.Ala198Ser missense_variant 0.4
rpsA 1833622 c.85delA frameshift_variant 0.12
rpsA 1834370 p.Lys277Gln missense_variant 0.25
rpsA 1834432 c.891G>A synonymous_variant 0.33
rpsA 1834807 c.1266G>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918218 c.279C>T synonymous_variant 0.14
tlyA 1918236 c.297A>G synonymous_variant 0.15
ndh 2101694 p.Ala450Asp missense_variant 0.29
ndh 2102124 p.Pro307Thr missense_variant 0.14
ndh 2102235 p.Glu270Lys missense_variant 0.12
ndh 2102252 p.Gly264Val missense_variant 0.13
ndh 2102613 p.Ala144Thr missense_variant 0.14
katG 2153927 p.Asp729Asn missense_variant 0.12
katG 2154582 c.1530C>A synonymous_variant 0.22
katG 2155023 c.1089C>A synonymous_variant 0.12
katG 2155389 c.723C>G synonymous_variant 1.0
katG 2155455 c.657G>T synonymous_variant 0.12
katG 2155653 c.459G>A synonymous_variant 0.18
katG 2155683 p.Lys143Asn missense_variant 0.22
PPE35 2169404 p.Asn403Lys missense_variant 0.18
PPE35 2170529 c.84G>T synonymous_variant 0.13
PPE35 2170627 c.-16_-15insC upstream_gene_variant 0.12
PPE35 2170648 c.-36C>A upstream_gene_variant 0.13
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2222001 c.1164C>T synonymous_variant 0.17
Rv1979c 2222220 c.945C>T synonymous_variant 0.17
Rv1979c 2222311 p.Ser285Leu missense_variant 0.12
Rv1979c 2222318 p.Ala283Ser missense_variant 0.14
Rv1979c 2222509 p.Ser219Leu missense_variant 0.15
Rv1979c 2223199 c.-35C>A upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223312 c.-148C>A upstream_gene_variant 0.15
pncA 2289445 c.-204C>A upstream_gene_variant 0.12
pncA 2289606 c.-365G>A upstream_gene_variant 0.2
pncA 2290024 c.-783C>T upstream_gene_variant 0.29
kasA 2519328 p.Gly405Asp missense_variant 0.12
eis 2715360 c.-28G>A upstream_gene_variant 0.22
ahpC 2726027 c.-166C>T upstream_gene_variant 0.14
ahpC 2726047 c.-146C>T upstream_gene_variant 0.14
folC 2746452 p.Gly383Ser missense_variant 0.2
folC 2747600 c.-2C>A upstream_gene_variant 0.12
pepQ 2860188 c.231C>A synonymous_variant 0.2
ribD 2986682 c.-157G>T upstream_gene_variant 0.18
ribD 2986733 c.-106C>T upstream_gene_variant 0.2
ribD 2987514 p.Arg226Tyr missense_variant 0.15
Rv2752c 3067120 c.-930_-929delACinsGA upstream_gene_variant 0.17
Rv2752c 3067155 c.-964C>A upstream_gene_variant 0.2
thyX 3067220 c.726G>A synonymous_variant 0.2
thyX 3067328 c.618G>A synonymous_variant 0.14
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3074229 p.Asp81Glu missense_variant 0.14
ald 3087499 p.Gly227Val missense_variant 0.15
fbiD 3339278 p.Gly54Asp missense_variant 0.15
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473833 c.-174G>T upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Cys missense_variant 0.12
fprA 3474646 p.Glu214* stop_gained 0.13
fprA 3474904 p.Gly300Arg missense_variant 0.15
fprA 3475096 p.Pro364Ser missense_variant 0.13
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612661 c.456G>A synonymous_variant 0.2
Rv3236c 3613001 p.Ala39Val missense_variant 0.17
fbiA 3640429 c.-114C>T upstream_gene_variant 0.33
fbiA 3641326 p.Val262Phe missense_variant 0.15
fbiB 3641448 c.-87G>A upstream_gene_variant 0.17
fbiB 3642239 c.705G>A synonymous_variant 0.22
alr 3841294 p.Gly43Cys missense_variant 0.12
rpoA 3877882 p.Ala209Glu missense_variant 0.15
rpoA 3878044 p.Ser155* stop_gained 0.2
rpoA 3878065 p.Pro148Gln missense_variant 0.22
rpoA 3878363 p.Ala49Ser missense_variant 0.17
ddn 3986707 c.-137C>T upstream_gene_variant 0.22
clpC1 4038632 p.Glu691Asp missense_variant 0.14
clpC1 4038991 p.Gly572Cys missense_variant 0.14
clpC1 4039547 c.1158C>A synonymous_variant 0.17
clpC1 4040246 c.459C>T synonymous_variant 0.17
clpC1 4040515 p.Glu64Lys missense_variant 0.12
clpC1 4040539 c.166C>T synonymous_variant 0.12
embC 4241247 p.Arg462Leu missense_variant 0.18
embC 4241256 p.Arg465Lys missense_variant 0.17
embC 4242063 p.Trp734* stop_gained 0.18
embC 4242344 p.Ala828Thr missense_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242704 p.Asp948Asn missense_variant 0.29
embC 4243082 p.Asp1074Asn missense_variant 0.18
embA 4243310 c.78G>T synonymous_variant 0.22
embA 4244007 p.Ala259Thr missense_variant 0.25
embA 4244568 p.Arg446Cys missense_variant 0.17
embA 4244727 p.Phe499Leu missense_variant 0.13
embA 4245191 c.1959G>T synonymous_variant 0.12
embB 4245824 c.-690G>T upstream_gene_variant 0.22
embB 4245854 c.-660C>A upstream_gene_variant 0.22
embB 4246566 p.Gly18Val missense_variant 0.2
embB 4247458 p.Tyr315* stop_gained 0.15
embB 4247671 c.1158G>A synonymous_variant 0.22
embB 4247690 p.Thr393Ala missense_variant 0.17
embB 4247784 p.Arg424Gln missense_variant 0.18
embB 4247952 p.Ser480Leu missense_variant 0.14
embB 4248040 c.1527C>T synonymous_variant 0.2
embB 4248724 p.Trp737* stop_gained 0.12
embB 4249514 p.Leu1001Met missense_variant 0.18
aftB 4266975 p.Pro621His missense_variant 0.25
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4267274 c.1563G>T synonymous_variant 0.12
aftB 4267516 p.Ala441Ser missense_variant 0.2
aftB 4267785 p.Gly351Val missense_variant 0.13
aftB 4268226 p.Ala204Glu missense_variant 0.22
aftB 4268354 c.483G>T synonymous_variant 0.5
aftB 4268486 p.Met117Ile missense_variant 0.2
ubiA 4269094 p.Trp247* stop_gained 0.33
ubiA 4269901 c.-68C>T upstream_gene_variant 0.17
ethA 4326719 p.Ala252Asp missense_variant 0.12
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
ethA 4328256 c.-783G>T upstream_gene_variant 0.14
ethA 4328433 c.-960G>T upstream_gene_variant 0.18
whiB6 4338539 c.-18G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0