TB-Profiler result

Run: ERR2229382
Summary

Run ID: ERR2229382

Sample name:

Date: 31-03-2023 17:08:45

Number of reads: 1026500

Percentage reads mapped: 98.87

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 6347 p.Gln370* stop_gained 0.13
gyrB 6657 p.Ser473* stop_gained 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576111 p.Ala255Gly missense_variant 0.25
mshA 576241 c.894C>A synonymous_variant 0.22
rpoB 760643 c.842delC frameshift_variant 0.2
rpoC 764343 p.Arg325His missense_variant 0.15
rpoC 764352 p.Val328Ala missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775677 p.Lys935Arg missense_variant 0.12
mmpL5 775680 p.Gly934Val missense_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801194 p.Arg129Gln missense_variant 0.15
fbiC 1303308 c.378C>T synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304151 p.Asp407Glu missense_variant 0.17
Rv1258c 1407232 p.Arg37Ser missense_variant 0.18
embR 1417060 c.287delC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.46
inhA 1674529 p.Asp110His missense_variant 0.12
rpsA 1834061 p.Ile174Val missense_variant 0.12
rpsA 1834499 c.958C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918105 p.Thr56Ser missense_variant 0.12
ndh 2102329 p.Lys238Asn missense_variant 0.29
katG 2153970 p.Asp714Glu missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.85
PPE35 2170053 p.Thr187Ser missense_variant 0.85
PPE35 2170406 c.207A>G synonymous_variant 0.18
PPE35 2170412 c.201G>C synonymous_variant 0.18
PPE35 2170415 c.198A>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290080 c.-839T>A upstream_gene_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
kasA 2519234 p.Glu374* stop_gained 0.29
pepQ 2859947 p.Val158Met missense_variant 0.17
Rv2752c 3064822 p.Val457Ala missense_variant 0.15
Rv2752c 3064825 p.Asp456Val missense_variant 0.15
Rv2752c 3064828 p.Gly455Asp missense_variant 0.15
thyX 3067888 p.Pro20Thr missense_variant 0.2
thyX 3068008 c.-63G>A upstream_gene_variant 0.2
thyA 3074296 p.Leu59Pro missense_variant 0.14
fbiD 3339410 p.Ala98Gly missense_variant 0.12
fbiD 3339578 p.Phe154Ser missense_variant 0.25
fprA 3474786 c.780C>A synonymous_variant 0.13
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.15
Rv3236c 3612988 c.129A>G synonymous_variant 0.12
fbiA 3640826 p.Tyr95Phe missense_variant 0.14
fbiB 3642024 p.Ala164Thr missense_variant 0.13
alr 3840299 c.1122C>T synonymous_variant 0.12
alr 3840591 p.Val277Gly missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877850 p.Gly220Cys missense_variant 0.2
rpoA 3877865 p.Leu215Met missense_variant 0.25
clpC1 4038275 p.Glu810Asp missense_variant 0.12
clpC1 4039682 c.1023C>T synonymous_variant 0.12
clpC1 4039691 c.1014G>C synonymous_variant 0.13
clpC1 4039714 p.Tyr331His missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.52
embB 4246556 p.Ala15Pro missense_variant 0.55
embB 4246563 p.Leu17Trp missense_variant 0.57
embB 4246567 c.54G>T synonymous_variant 0.6
embB 4246781 p.Ala90Pro missense_variant 0.11
embB 4247066 p.Ile185Val missense_variant 0.2
embB 4248624 p.Thr704Ile missense_variant 0.14
aftB 4267895 c.942C>T synonymous_variant 0.25
ethA 4328430 c.-957A>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0