TB-Profiler result

Run: ERR2229395
Summary

Run ID: ERR2229395

Sample name:

Date: 31-03-2023 17:10:00

Number of reads: 896231

Percentage reads mapped: 98.84

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 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 6882 p.Leu548Ser missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8071 p.Val257Ala missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.54
mshA 576111 p.Ala255Gly missense_variant 0.27
ccsA 620638 c.751delG frameshift_variant 0.22
rpoB 759741 c.-66C>T upstream_gene_variant 0.11
rpoB 759794 c.-13G>A upstream_gene_variant 0.25
rpoB 760668 p.Thr288Ala missense_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 761585 p.His593Gln missense_variant 0.12
rpoC 763381 c.12C>A synonymous_variant 0.15
rpoC 764346 p.Pro326Leu missense_variant 0.33
rpoC 765356 p.Met663Leu missense_variant 0.22
rpoC 766403 c.3035delT frameshift_variant 0.22
rpoC 766995 p.Gly1209Val missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.14
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.14
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.12
mmpS5 778630 p.Leu92Phe missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304426 p.Leu499Arg missense_variant 0.2
fbiC 1304751 c.1821C>A synonymous_variant 0.12
fbiC 1305213 c.2283C>A synonymous_variant 0.17
fbiC 1305242 c.2315delT frameshift_variant 0.12
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.13
Rv1258c 1406946 p.Ala132Gly missense_variant 0.13
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.15
Rv1258c 1407063 p.Ala93Glu missense_variant 0.17
embR 1416526 c.822C>G synonymous_variant 0.15
embR 1416585 p.Leu255Met missense_variant 0.15
embR 1416779 p.Val190Ala missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
rpsA 1833815 p.Thr92Ser missense_variant 0.15
rpsA 1834095 p.Leu185Pro missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101917 p.Phe376Leu missense_variant 0.14
ndh 2102572 c.471A>G synonymous_variant 0.11
ndh 2102935 c.108C>T synonymous_variant 0.18
katG 2154820 p.Val431Ala missense_variant 0.17
katG 2154887 p.Ala409Thr missense_variant 0.18
katG 2155256 p.Pro286Thr missense_variant 0.2
katG 2155404 p.Asn236Lys missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169293 c.1320T>C synonymous_variant 0.19
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.81
PPE35 2170053 p.Thr187Ser missense_variant 0.83
Rv1979c 2223035 p.Gly44Arg missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289960 c.-719C>A upstream_gene_variant 0.12
kasA 2518809 p.Lys232Arg missense_variant 0.22
kasA 2518864 c.750G>C synonymous_variant 0.36
folC 2746468 c.1131G>A synonymous_variant 0.17
folC 2747008 c.591C>A synonymous_variant 0.17
pepQ 2859469 p.Leu317Pro missense_variant 0.14
Rv2752c 3064917 p.Asn425Lys missense_variant 0.22
Rv2752c 3065045 p.Phe383Ile missense_variant 0.17
Rv2752c 3066332 c.-141C>A upstream_gene_variant 0.14
fbiD 3339374 p.Glu86Ala missense_variant 0.11
fbiD 3339408 c.291C>T synonymous_variant 0.14
fbiD 3339571 p.Cys152Ser missense_variant 0.15
whiB7 3568428 c.252A>G synonymous_variant 0.2
Rv3236c 3612700 p.Asp139Glu missense_variant 0.15
fbiB 3641648 c.114G>T synonymous_variant 0.12
fbiB 3642093 c.559T>C synonymous_variant 0.2
fbiB 3642394 p.Pro287Gln missense_variant 0.12
alr 3840551 c.870G>T synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878599 c.-92C>G upstream_gene_variant 0.67
embC 4241437 c.1575C>T synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243189 c.-44C>A upstream_gene_variant 0.15
embA 4244184 p.Ser318Leu missense_variant 0.12
embA 4245875 p.Lys881Asn missense_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.8
embB 4246556 p.Ala15Pro missense_variant 0.8
embB 4246563 p.Leu17Trp missense_variant 0.73
embB 4246567 c.54G>T synonymous_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407640 p.Val188Ala missense_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0