TB-Profiler result

Run: ERR2229361
Summary

Run ID: ERR2229361

Sample name:

Date: 31-03-2023 17:06:08

Number of reads: 835549

Percentage reads mapped: 98.7

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 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
katG 2155165 p.Gly316Asp missense_variant 0.13 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 6207 p.Ala323Val missense_variant 0.14
gyrB 6959 p.Gln574* stop_gained 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8243 p.Ile314Met missense_variant 0.11
mshA 575363 p.His6Asn missense_variant 0.18
mshA 575384 p.Ile13Val missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.4
rpoB 761418 p.Ala538Thr missense_variant 0.15
rpoC 764101 c.732C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.17
mmpL5 777221 p.Tyr420* stop_gained 0.2
mmpL5 777449 c.1032C>T synonymous_variant 0.15
mmpR5 778328 c.-662C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800701 c.-108G>T upstream_gene_variant 0.13
fbiC 1303476 c.546G>T synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304155 p.Arg409Trp missense_variant 0.15
fbiC 1305274 p.Ser782Pro missense_variant 0.13
Rv1258c 1407157 p.Ala62Pro missense_variant 0.11
atpE 1461043 c.-2A>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
rpsA 1834422 p.Gly294Val missense_variant 0.25
rpsA 1834562 p.Gly341Cys missense_variant 0.16
tlyA 1917784 c.-156C>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102003 p.Ile347Thr missense_variant 0.11
ndh 2102776 c.267C>T synonymous_variant 0.17
ndh 2102854 p.Ile63Leu missense_variant 0.11
ndh 2102857 c.186T>C synonymous_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.21
katG 2155191 c.921A>C synonymous_variant 0.21
PPE35 2167745 p.Thr956Arg missense_variant 0.36
PPE35 2167859 c.2754T>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168976 p.Ala546Asp missense_variant 0.13
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.6
Rv1979c 2221954 p.His404Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290111 c.-870G>T upstream_gene_variant 0.18
kasA 2518864 c.750G>C synonymous_variant 0.13
eis 2715100 p.Pro78Gln missense_variant 0.13
ahpC 2725948 c.-245C>A upstream_gene_variant 0.17
ahpC 2726309 c.117C>A synonymous_variant 0.13
ahpC 2726374 p.Cys61Phe missense_variant 0.15
folC 2746229 c.1369delG frameshift_variant 0.25
folC 2746587 p.Arg338Trp missense_variant 0.17
folC 2746929 p.Pro224Thr missense_variant 0.2
pepQ 2860162 p.Arg86Leu missense_variant 0.15
pepQ 2860304 p.Ser39Ala missense_variant 0.25
Rv2752c 3065022 c.1170G>T synonymous_variant 0.12
Rv2752c 3065214 c.978C>T synonymous_variant 0.15
Rv2752c 3065513 p.Arg227Trp missense_variant 0.14
thyX 3068011 c.-66C>T upstream_gene_variant 0.12
ald 3087348 p.Gly177Ser missense_variant 0.12
fbiD 3339430 p.Glu105Lys missense_variant 0.17
fprA 3473917 c.-90T>A upstream_gene_variant 0.17
fprA 3474319 p.Gly105Cys missense_variant 0.33
whiB7 3568582 p.Pro33Gln missense_variant 0.12
whiB7 3568624 p.Pro19Leu missense_variant 0.12
Rv3236c 3612693 p.Arg142Gly missense_variant 0.15
fbiA 3641307 p.Met255Ile missense_variant 0.18
fbiB 3642009 p.Gly159Ser missense_variant 0.12
fbiB 3642047 c.513G>T synonymous_variant 0.2
fbiB 3642471 p.Met313Val missense_variant 0.15
fbiB 3642687 p.Leu385Val missense_variant 0.11
rpoA 3877602 p.His302Gln missense_variant 0.13
rpoA 3878310 c.198G>A synonymous_variant 0.12
clpC1 4038519 p.Arg729Leu missense_variant 0.22
clpC1 4038575 c.2130C>T synonymous_variant 0.2
clpC1 4039003 p.Asn568Tyr missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.12
clpC1 4039654 p.Thr351Ser missense_variant 0.13
embC 4240651 c.789G>T synonymous_variant 0.2
embC 4240783 c.921G>T synonymous_variant 0.12
embC 4242581 p.Ala907Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242725 p.Gln955Lys missense_variant 0.18
embA 4243440 p.Leu70Met missense_variant 0.13
embA 4245165 p.Pro645Thr missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.46
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246567 c.54_55insT frameshift_variant 0.33
embB 4248610 p.Ile699Met missense_variant 0.25
embB 4249000 c.2487T>A synonymous_variant 0.18
aftB 4267277 c.1560G>T synonymous_variant 0.14
aftB 4267910 c.927G>A synonymous_variant 0.17
aftB 4268658 p.Ser60* stop_gained 0.25
ubiA 4269208 p.Ser209* stop_gained 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338705 c.-184A>G upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0