TB-Profiler result

Run: ERR2229589
Summary

Run ID: ERR2229589

Sample name:

Date: 31-03-2023 17:20:23

Number of reads: 558050

Percentage reads mapped: 99.01

Strain: lineage4.8

Drug-resistance: HR-TB

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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 0.99
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
katG 2155627 c.484delG frameshift_variant 0.4 isoniazid
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 6139 c.900G>T synonymous_variant 0.29
gyrB 6567 p.Ala443Val missense_variant 0.29
gyrB 6623 p.Ser462Thr missense_variant 0.18
gyrA 6721 c.-581C>T upstream_gene_variant 0.12
gyrA 6832 c.-470C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8115 p.Thr272Ala missense_variant 0.29
fgd1 490722 c.-61G>T upstream_gene_variant 0.15
fgd1 491500 p.Glu240* stop_gained 0.22
fgd1 491512 p.Asn244His missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576242 p.Gly299Ser missense_variant 1.0
mshA 576641 p.Asn432His missense_variant 0.25
ccsA 620186 p.Gly99Val missense_variant 0.13
ccsA 620363 p.Ala158Asp missense_variant 0.18
rpoB 760266 p.Met154Leu missense_variant 0.17
rpoB 761710 p.Val635Asp missense_variant 0.13
rpoB 762020 p.Glu738Asp missense_variant 0.33
rpoB 762852 p.Pro1016Thr missense_variant 0.14
rpoC 763043 c.-327G>T upstream_gene_variant 0.13
rpoC 763532 p.Thr55Ser missense_variant 0.12
rpoC 763850 p.Ala161Ser missense_variant 0.18
rpoC 764010 p.Arg214His missense_variant 0.22
rpoC 764279 p.Gln304Lys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.18
mmpL5 775931 c.2550C>T synonymous_variant 0.18
mmpL5 776487 p.Gln665Arg missense_variant 0.12
mmpL5 776537 p.Met648Ile missense_variant 0.15
mmpL5 776597 p.Asp628Glu missense_variant 0.22
mmpL5 776865 p.Met539Thr missense_variant 0.12
mmpL5 776987 c.1494G>T synonymous_variant 0.19
mmpL5 777164 c.1317C>T synonymous_variant 0.17
mmpL5 777348 p.Gly378Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800653 c.-156A>G upstream_gene_variant 0.18
rplC 800669 c.-140G>T upstream_gene_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304125 p.Val399Leu missense_variant 0.25
fbiC 1304203 p.Ala425Ser missense_variant 0.15
Rv1258c 1406286 p.Met352Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473887 n.230T>C non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476044 n.2387T>C non_coding_transcript_exon_variant 0.29
fabG1 1673355 c.-85A>T upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
fabG1 1673945 p.Arg169Pro missense_variant 0.25
rpsA 1833431 c.-111T>G upstream_gene_variant 0.18
rpsA 1834188 p.Val216Ala missense_variant 0.4
rpsA 1834382 p.Glu281* stop_gained 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102653 p.His130Glu missense_variant 0.33
katG 2154092 p.Asp674Tyr missense_variant 0.14
katG 2154771 p.His447Gln missense_variant 0.25
katG 2155659 c.453C>A synonymous_variant 0.2
katG 2156260 c.-149C>A upstream_gene_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.26
PPE35 2167967 c.2646A>C synonymous_variant 0.26
PPE35 2167997 c.2616G>C synonymous_variant 0.15
PPE35 2168409 p.Thr735Ile missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168838 p.Pro592Gln missense_variant 0.17
PPE35 2168953 p.Asn554Asp missense_variant 0.2
PPE35 2169044 c.1569G>C synonymous_variant 0.25
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.12
PPE35 2169293 c.1320T>C synonymous_variant 0.2
PPE35 2169602 c.1011C>A synonymous_variant 0.25
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.67
PPE35 2170147 p.Ser156Ala missense_variant 0.27
PPE35 2170518 p.Asp32Ala missense_variant 0.12
PPE35 2170544 c.69G>A synonymous_variant 0.17
PPE35 2170547 c.66A>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289857 c.-616A>T upstream_gene_variant 0.4
kasA 2518809 p.Lys232Arg missense_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.14
kasA 2519153 p.Ile347Val missense_variant 0.14
eis 2714658 c.675G>A synonymous_variant 0.22
eis 2715336 c.-4T>C upstream_gene_variant 0.15
folC 2747364 p.Ala79Ser missense_variant 0.14
Rv2752c 3067187 c.-996C>A upstream_gene_variant 0.17
thyX 3067854 c.89_91delACG disruptive_inframe_deletion 0.18
thyA 3073713 c.759G>A synonymous_variant 0.13
thyA 3074098 p.Ser125Phe missense_variant 0.67
thyA 3074551 c.-80C>A upstream_gene_variant 0.29
ald 3087193 p.Gly125Ala missense_variant 0.33
ald 3087220 p.Ser134Asn missense_variant 0.22
ald 3087459 p.Arg214Trp missense_variant 0.25
fbiD 3339207 c.90C>T synonymous_variant 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474633 c.627G>T synonymous_variant 0.14
Rv3236c 3612688 c.429C>A synonymous_variant 0.29
Rv3236c 3612854 p.His88Pro missense_variant 0.22
Rv3236c 3613005 p.Leu38Met missense_variant 0.17
fbiB 3641951 c.417G>A synonymous_variant 0.33
fbiB 3642053 c.519G>T synonymous_variant 0.29
fbiB 3642770 c.1236G>T synonymous_variant 0.29
alr 3840649 p.Tyr258Asp missense_variant 0.25
alr 3840770 c.651C>T synonymous_variant 0.5
alr 3841546 c.-126C>A upstream_gene_variant 0.43
rpoA 3878307 c.201C>A synonymous_variant 0.15
ddn 3986848 p.Pro2Leu missense_variant 0.12
clpC1 4038220 p.Glu829* stop_gained 0.33
clpC1 4039018 p.Ser563Ala missense_variant 0.2
clpC1 4039022 c.1683A>G synonymous_variant 0.18
clpC1 4039838 c.867G>T synonymous_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.4
clpC1 4040540 c.165G>C synonymous_variant 0.5
embC 4239796 c.-67C>A upstream_gene_variant 0.15
embC 4240426 c.564C>A synonymous_variant 0.33
embC 4240435 p.Tyr191* stop_gained 0.67
embC 4241104 p.Glu414Asp missense_variant 0.2
embC 4242499 p.Arg879Ser missense_variant 0.18
embA 4242553 c.-680G>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242685 c.-548C>T upstream_gene_variant 0.17
embA 4243294 p.Gly21Val missense_variant 0.33
embA 4245787 p.Ala852Asp missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246785 p.Met91Lys missense_variant 0.25
embB 4246991 p.Asn160Tyr missense_variant 0.33
embB 4247156 p.Thr215Pro missense_variant 0.5
embB 4249146 p.Thr878Ile missense_variant 0.12
embB 4249371 p.Leu953Gln missense_variant 0.17
embB 4249502 p.Gln997Lys missense_variant 0.15
aftB 4267825 p.Val338Leu missense_variant 0.33
aftB 4268346 p.Ala164Asp missense_variant 0.22
aftB 4268854 c.-18G>T upstream_gene_variant 0.2
aftB 4269000 c.-164G>A upstream_gene_variant 0.33
ethR 4326961 c.-588G>C upstream_gene_variant 0.29
ethR 4326964 c.-585G>A upstream_gene_variant 0.29
ethR 4326970 c.-579G>T upstream_gene_variant 0.25
ethA 4327188 p.Arg96Gly missense_variant 0.25
ethR 4328092 p.Thr182Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0