TB-Profiler result

Run: ERR2229802
Summary

Run ID: ERR2229802

Sample name:

Date: 31-03-2023 17:36:50

Number of reads: 964458

Percentage reads mapped: 99.23

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575816 p.Leu157Met missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.29
rpoB 761658 p.Pro618Ser missense_variant 0.14
rpoC 765917 p.Phe850Ile missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775802 p.Met893Ile missense_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777164 c.1317C>T synonymous_variant 0.14
mmpL5 778873 c.-393G>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801232 p.Gln142Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303920 c.990C>A synonymous_variant 0.15
fbiC 1305091 p.Ala721Ser missense_variant 0.12
embR 1417293 c.55T>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476169 n.2512A>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
inhA 1674740 p.Gly180Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102367 p.Ala226Pro missense_variant 0.13
ndh 2102368 c.675C>T synonymous_variant 0.13
ndh 2102599 c.444T>C synonymous_variant 0.14
ndh 2102604 c.439T>C synonymous_variant 0.12
ndh 2102610 c.433T>C synonymous_variant 0.12
ndh 2102638 c.405A>G synonymous_variant 0.12
ndh 2102683 c.360T>C synonymous_variant 0.18
ndh 2102813 p.Arg77Leu missense_variant 0.25
katG 2154948 c.1164G>A synonymous_variant 0.13
katG 2156425 c.-314G>T upstream_gene_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.19
PPE35 2168150 c.2463T>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170082 c.531T>C synonymous_variant 0.12
Rv1979c 2222892 c.273C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289876 c.-635G>A upstream_gene_variant 0.14
kasA 2518071 c.-44G>A upstream_gene_variant 0.14
kasA 2519128 c.1014G>C synonymous_variant 0.17
kasA 2519131 c.1017G>C synonymous_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.18
eis 2715155 p.Gly60Trp missense_variant 0.18
folC 2747008 c.591C>A synonymous_variant 0.2
folC 2747741 c.-143G>A upstream_gene_variant 0.12
Rv2752c 3064798 p.Arg465Leu missense_variant 0.12
Rv2752c 3065533 p.Pro220Gln missense_variant 0.25
Rv2752c 3066172 p.Pro7Gln missense_variant 0.15
Rv2752c 3066174 c.18C>A synonymous_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.29
ald 3087424 p.Asp202Val missense_variant 0.12
fbiB 3642738 p.Ile402Phe missense_variant 0.17
alr 3840730 p.Val231Leu missense_variant 0.14
rpoA 3878587 c.-80T>G upstream_gene_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039003 p.Asn568Asp missense_variant 0.15
clpC1 4039161 p.His515Gly missense_variant 0.11
clpC1 4039714 p.Tyr331His missense_variant 0.13
clpC1 4040160 p.Ala182Val missense_variant 0.12
clpC1 4040571 p.Ala45Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244046 p.Ser272Pro missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246747 p.Asp78Glu missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.23
embB 4248717 p.Asn735Thr missense_variant 0.2
embB 4249758 p.Thr1082Asn missense_variant 0.13
aftB 4268535 p.Gly101Val missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407710 p.Glu165* stop_gained 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0