TB-Profiler result

Run: ERR2229188
Summary

Run ID: ERR2229188

Sample name:

Date: 31-03-2023 16:47:14

Number of reads: 980428

Percentage reads mapped: 99.2

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 576005 p.Glu220* stop_gained 0.13
mshA 576591 p.Arg415Leu missense_variant 0.18
rpoC 765775 c.2406C>T synonymous_variant 0.14
rpoC 766860 p.Arg1164Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778598 p.Ile103Thr missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303580 p.Thr217Met missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304866 p.Gly646Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472469 n.624G>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.29
PPE35 2167967 c.2646A>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169143 c.1470G>T synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169748 p.Ile289Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.14
folC 2746244 p.Ala452Asp missense_variant 0.2
folC 2746411 c.1188G>T synonymous_variant 0.12
folC 2746879 p.Lys240Asn missense_variant 0.17
Rv2752c 3064666 p.Arg509Pro missense_variant 0.11
Rv2752c 3064850 c.1341dupG frameshift_variant 0.15
Rv2752c 3064855 p.Lys446Arg missense_variant 0.17
Rv3236c 3613194 c.-78C>A upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
clpC1 4038504 p.Met734Lys missense_variant 0.16
embC 4240801 c.939C>T synonymous_variant 0.13
embC 4240803 p.Tyr314Phe missense_variant 0.14
embC 4241660 p.Leu600Met missense_variant 0.17
embA 4242322 c.-911C>T upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243173 c.-60A>G upstream_gene_variant 0.12
embA 4244137 p.Ala302Glu missense_variant 0.12
embA 4245398 p.Asn722Lys missense_variant 0.17
embB 4246915 c.402C>T synonymous_variant 0.13
aftB 4268850 c.-14T>C upstream_gene_variant 0.15
aftB 4268873 c.-37C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0