TB-Profiler result

Run: ERR2229599
Summary

Run ID: ERR2229599

Sample name:

Date: 31-03-2023 17:20:49

Number of reads: 985200

Percentage reads mapped: 99.19

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 576108 p.Ala254Gly missense_variant 0.2
ccsA 620117 p.Val76Gly missense_variant 0.4
rpoB 761427 p.Pro541Thr missense_variant 0.18
rpoC 763927 c.558C>T synonymous_variant 0.17
rpoC 763992 p.Ile208Thr missense_variant 0.11
rpoC 764542 c.1173C>G synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776482 p.Ala667Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781550 c.-10A>G upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473330 n.1485A>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.17
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.17
fabG1 1674047 p.Leu203Pro missense_variant 0.21
fabG1 1674139 p.Gly234Arg missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.26
PPE35 2168047 p.Leu856Val missense_variant 0.21
PPE35 2168051 p.Val854Ile missense_variant 0.17
PPE35 2168196 p.Leu806Pro missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169149 c.1464G>T synonymous_variant 0.21
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169337 p.Asp426His missense_variant 0.13
PPE35 2169341 c.1272A>T synonymous_variant 0.13
PPE35 2169902 c.711G>C synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.46
PPE35 2170400 c.213G>C synonymous_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289301 c.-60T>C upstream_gene_variant 0.13
pncA 2289755 c.-514G>A upstream_gene_variant 0.12
pncA 2289942 c.-702delT upstream_gene_variant 0.17
kasA 2518575 p.Ile154Thr missense_variant 0.1
folC 2746599 c.979_999delCGGGCCGGCTTTGCCGCCGTC conservative_inframe_deletion 0.25
Rv2752c 3065803 p.Glu130Val missense_variant 0.12
Rv2752c 3065821 p.Val124Glu missense_variant 0.12
thyX 3067647 p.Ser100Tyr missense_variant 0.15
fprA 3474144 p.Trp46Cys missense_variant 0.12
fbiA 3641392 p.Ile284Leu missense_variant 0.17
alr 3840769 p.Phe218Leu missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.3
rpoA 3877644 p.Asn288Lys missense_variant 0.13
rpoA 3877947 c.561C>A synonymous_variant 0.17
rpoA 3877958 p.Glu184* stop_gained 0.15
rpoA 3878281 p.Ile76Thr missense_variant 0.12
clpC1 4039486 p.Gly407Ser missense_variant 0.13
panD 4043990 p.Ala98Thr missense_variant 0.14
embC 4241789 p.Val643Leu missense_variant 0.11
embC 4242138 p.Leu759Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244829 p.Phe533Leu missense_variant 0.22
embA 4246507 p.Ala1092Glu missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.32
embB 4246556 p.Ala15Pro missense_variant 0.32
embB 4246563 p.Leu17Trp missense_variant 0.24
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4249725 p.Val1071Ala missense_variant 0.18
aftB 4267499 c.1336_1337delCC frameshift_variant 0.11
ubiA 4269955 c.-122T>C upstream_gene_variant 0.11
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethA 4327344 p.Thr44Ser missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0