TB-Profiler result

Run: ERR2229377
Summary

Run ID: ERR2229377

Sample name:

Date: 31-03-2023 17:08:48

Number of reads: 977122

Percentage reads mapped: 98.8

Strain: lineage4.8

Drug-resistance: Other

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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
gid 4407997 p.Gly69Asp missense_variant 0.18 streptomycin
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 5626 p.Asn129Lys missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7564 c.266_268delACG disruptive_inframe_deletion 0.12
gyrA 8908 p.Ser536Ile missense_variant 0.17
gyrA 9068 c.1767G>A synonymous_variant 0.12
gyrA 9782 c.2483_2484delTG frameshift_variant 0.15
fgd1 491607 c.825G>T synonymous_variant 0.15
rpoB 760974 p.Met390Val missense_variant 0.17
rpoB 762208 p.Thr801Asn missense_variant 0.14
rpoC 764358 p.Leu330Arg missense_variant 0.25
rpoC 764988 p.Gln540Arg missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775981 p.Leu834Met missense_variant 0.22
mmpL5 775987 p.His832Tyr missense_variant 0.22
mmpL5 775990 c.2491C>T synonymous_variant 0.22
mmpL5 776003 c.2478C>T synonymous_variant 0.14
mmpR5 779002 p.Asp5Tyr missense_variant 0.14
mmpR5 779142 c.154dupT frameshift_variant 0.13
mmpL5 779148 c.-668C>G upstream_gene_variant 0.13
mmpR5 779207 p.Met73Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801141 c.333C>T synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304208 c.1278C>A synonymous_variant 0.18
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.2
Rv1258c 1406946 p.Ala132Gly missense_variant 0.2
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472755 n.910G>T non_coding_transcript_exon_variant 0.12
rrs 1473381 n.1536C>G splice_region_variant&non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.46
fabG1 1673705 p.Ala89Val missense_variant 0.22
inhA 1674987 c.786C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101846 c.1197G>C synonymous_variant 0.25
ndh 2102417 p.Ala209Glu missense_variant 0.25
ndh 2102719 p.Tyr108* stop_gained 0.4
katG 2154774 c.1338C>T synonymous_variant 0.15
katG 2155191 c.921A>C synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.38
PPE35 2167760 c.2853G>A synonymous_variant 0.22
PPE35 2167763 p.Ile950Val missense_variant 0.22
PPE35 2167784 c.2829C>T synonymous_variant 0.18
PPE35 2167814 c.2799C>T synonymous_variant 0.33
PPE35 2168215 p.Thr800Ala missense_variant 0.33
PPE35 2168220 p.Ala798Glu missense_variant 0.33
PPE35 2168231 c.2382T>C synonymous_variant 0.33
PPE35 2168234 c.2379G>T synonymous_variant 0.29
PPE35 2168237 c.2376G>A synonymous_variant 0.25
PPE35 2168241 p.Ile791Thr missense_variant 0.2
PPE35 2168244 p.Ser790Thr missense_variant 0.2
PPE35 2168248 p.Leu789Ile missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.3
PPE35 2169272 c.1341C>G synonymous_variant 0.3
PPE35 2169278 c.1335T>C synonymous_variant 0.35
PPE35 2169281 c.1332T>G synonymous_variant 0.37
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.6
Rv1979c 2222580 c.585G>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.2
kasA 2518917 p.Ala268Asp missense_variant 0.25
eis 2714979 c.354G>A synonymous_variant 0.33
ahpC 2726667 p.Asp159Tyr missense_variant 0.17
folC 2747029 c.570G>T synonymous_variant 0.12
folC 2747389 c.210G>T synonymous_variant 0.12
pepQ 2859639 c.780T>G synonymous_variant 0.29
pepQ 2860578 c.-160G>T upstream_gene_variant 0.15
ribD 2987400 p.Arg188Cys missense_variant 0.25
Rv2752c 3065842 p.Arg117His missense_variant 0.11
thyX 3068011 c.-66C>T upstream_gene_variant 0.27
thyX 3068015 c.-70T>G upstream_gene_variant 0.27
thyX 3068114 c.-169G>T upstream_gene_variant 0.22
thyA 3074492 c.-21T>A upstream_gene_variant 0.25
thyA 3074641 c.-171delT upstream_gene_variant 0.14
whiB7 3568613 p.Gly23Ser missense_variant 0.14
fbiA 3640678 p.Asn46Tyr missense_variant 0.18
fbiA 3640880 p.Leu113Arg missense_variant 0.2
fbiA 3640888 c.349delC frameshift_variant 0.29
fbiB 3642506 p.Asp324Glu missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.16
rpoA 3877774 p.Ala245Glu missense_variant 0.33
clpC1 4039574 c.1131G>A synonymous_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.22
clpC1 4039829 p.Leu292Ile missense_variant 0.2
clpC1 4039850 c.855T>C synonymous_variant 0.17
panD 4044121 p.Arg54Gln missense_variant 0.22
embC 4240211 p.Val117Phe missense_variant 0.13
embC 4240584 p.Thr241Asn missense_variant 0.33
embC 4240985 p.Arg375Trp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242740 p.Leu960Phe missense_variant 0.2
embA 4243335 p.Pro35Thr missense_variant 0.2
embA 4243390 p.Gly53Val missense_variant 0.17
embA 4243705 p.Gly158Ala missense_variant 0.17
embA 4245399 p.Leu723Met missense_variant 0.4
embB 4245602 c.-912C>T upstream_gene_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.32
embB 4246548 p.Pro12Gln missense_variant 0.89
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247512 c.999T>C synonymous_variant 0.13
embB 4247516 p.Asn335Asp missense_variant 0.14
embB 4247994 p.Phe494Tyr missense_variant 0.18
embB 4249078 p.Gln855His missense_variant 0.17
embB 4249410 p.Pro966Gln missense_variant 0.12
aftB 4267901 c.936G>T synonymous_variant 0.5
aftB 4268354 c.483G>A synonymous_variant 0.17
aftB 4269081 c.-245G>T upstream_gene_variant 0.12
ethA 4326244 p.Asp410Glu missense_variant 0.13
ethA 4327519 c.-46C>T upstream_gene_variant 0.29
ethA 4327896 c.-423C>T upstream_gene_variant 0.13
ethA 4328052 c.-579G>T upstream_gene_variant 0.13
ethA 4328273 c.-801delT upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407782 p.Ala141Ser missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0