TB-Profiler result

Run: ERR2229316
Summary

Run ID: ERR2229316

Sample name:

Date: 31-03-2023 17:00:12

Number of reads: 713016

Percentage reads mapped: 95.42

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 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
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 7194 p.Met652Thr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7822 p.Leu174Arg missense_variant 0.22
gyrA 7883 c.582G>T synonymous_variant 0.15
fgd1 491099 p.Gly106Val missense_variant 0.17
fgd1 491639 p.Val286Ala missense_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.15
rpoC 763912 c.543G>C synonymous_variant 0.2
rpoC 764148 p.Ser260* stop_gained 0.29
rpoC 765260 p.Ala631Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775871 c.2610C>T synonymous_variant 0.33
mmpL5 775874 c.2607C>A synonymous_variant 0.38
mmpL5 776087 c.2394C>G synonymous_variant 0.33
mmpL5 776510 c.1971C>A synonymous_variant 0.25
mmpR5 778328 c.-662C>T upstream_gene_variant 0.17
mmpS5 778482 p.Ala142Ser missense_variant 0.14
mmpL5 778872 c.-392C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781665 p.Arg36Cys missense_variant 0.12
rplC 800618 c.-191T>C upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304296 p.Gln456* stop_gained 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
rpsA 1833960 p.Leu140Pro missense_variant 0.29
rpsA 1834757 p.Gly406* stop_gained 0.22
rpsA 1834795 p.Tyr418* stop_gained 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918296 c.357G>T synonymous_variant 0.15
ndh 2101769 p.Arg425Leu missense_variant 0.12
ndh 2101827 p.Gly406Trp missense_variant 0.2
ndh 2102264 p.Lys260Arg missense_variant 0.15
katG 2155378 p.Ala245Glu missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168871 p.Leu581Pro missense_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170189 p.Glu142Gln missense_variant 0.14
PPE35 2170403 c.210C>G synonymous_variant 0.19
PPE35 2170406 c.207A>G synonymous_variant 0.19
Rv1979c 2223278 c.-114G>C upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518403 p.Ser97Thr missense_variant 0.14
eis 2714324 p.Arg337Ser missense_variant 0.14
eis 2715424 c.-92C>T upstream_gene_variant 0.13
ahpC 2725995 c.-198A>G upstream_gene_variant 0.13
pepQ 2859604 p.Gly272Glu missense_variant 0.18
pepQ 2859791 p.Ala210Thr missense_variant 0.25
thyX 3067837 p.Glu37* stop_gained 0.2
thyX 3067863 p.Asp28Gly missense_variant 0.29
thyA 3073803 c.669G>A synonymous_variant 0.12
thyA 3074238 c.234C>A synonymous_variant 0.2
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568877 c.-198C>T upstream_gene_variant 0.18
Rv3236c 3611962 c.1155C>T synonymous_variant 0.15
fbiA 3640365 c.-178C>T upstream_gene_variant 0.17
fbiB 3641223 c.-312C>T upstream_gene_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.27
clpC1 4039452 p.Pro418Gln missense_variant 0.25
embC 4240581 p.Leu240His missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243144 c.-89C>A upstream_gene_variant 0.13
embA 4243703 c.471C>T synonymous_variant 0.14
embA 4244223 p.Ala331Pro missense_variant 0.29
embA 4244934 p.Thr568Pro missense_variant 0.18
embA 4245083 c.1851A>G synonymous_variant 0.18
embA 4245095 c.1863C>A synonymous_variant 0.17
embA 4246020 p.Ala930Ser missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.58
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4247470 c.957T>C synonymous_variant 0.18
embB 4247472 p.Phe320Tyr missense_variant 0.18
embB 4247805 p.Ala431Val missense_variant 0.13
embB 4249083 p.Thr857Lys missense_variant 0.15
embB 4249186 c.2673G>T synonymous_variant 0.12
aftB 4267900 p.Ala313Ser missense_variant 0.33
aftB 4268478 p.Ala120Val missense_variant 0.12
aftB 4268776 p.Ser21Gly missense_variant 0.18
aftB 4268906 c.-70C>A upstream_gene_variant 0.14
aftB 4269201 c.-365A>G upstream_gene_variant 0.17
aftB 4269771 c.-935C>T upstream_gene_variant 0.15
ethR 4328169 p.Trp207Cys missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0