TB-Profiler result

Run: ERR2229657
Summary

Run ID: ERR2229657

Sample name:

Date: 31-03-2023 17:23:51

Number of reads: 909146

Percentage reads mapped: 99.4

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 6035 p.Arg266Ser missense_variant 0.12
gyrA 6403 c.-899T>C upstream_gene_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7777 p.Arg159Leu missense_variant 0.11
ccsA 620033 p.Ala48Asp missense_variant 0.11
rpoB 761296 p.Tyr497Phe missense_variant 0.11
rpoC 764059 c.690G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775834 p.Ala883Ser missense_variant 0.12
mmpL5 778522 c.-42A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407413 c.-73C>G upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471776 n.-70G>T upstream_gene_variant 0.12
rrs 1473146 n.1301G>C non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474425 n.768A>T non_coding_transcript_exon_variant 0.33
rrl 1475499 n.1842C>A non_coding_transcript_exon_variant 0.29
rrl 1475789 n.2132C>A non_coding_transcript_exon_variant 0.17
rrl 1476114 n.2457T>C non_coding_transcript_exon_variant 0.67
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
inhA 1673574 c.-628C>A upstream_gene_variant 0.12
rpsA 1833544 c.3G>A start_lost 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154485 p.Leu543Ile missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.1
PPE35 2169281 c.1332T>G synonymous_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2222517 c.648C>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715116 p.Gly73Ser missense_variant 0.12
Rv2752c 3064904 p.Asp430Tyr missense_variant 0.17
Rv2752c 3065255 p.Ser313Thr missense_variant 0.13
Rv2752c 3065638 p.Leu185Pro missense_variant 0.1
Rv3236c 3612658 c.459G>T synonymous_variant 0.18
alr 3840825 p.Tyr199Cys missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.12
embC 4242053 p.Tyr731Asn missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326099 p.Gln459* stop_gained 0.14
ethA 4326110 p.Trp455Leu missense_variant 0.15
ethA 4327329 p.Arg49Ser missense_variant 0.2
ethA 4327442 p.Gly11Asp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408019 p.Gly62Cys missense_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0