TB-Profiler result

Run: ERR2229371
Summary

Run ID: ERR2229371

Sample name:

Date: 31-03-2023 17:07:26

Number of reads: 978124

Percentage reads mapped: 98.8

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 7160 p.Ala641Thr missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8668 p.Ala456Asp missense_variant 0.17
gyrA 9221 c.1920C>T synonymous_variant 0.22
fgd1 490957 p.Thr59Ser missense_variant 0.14
fgd1 491066 c.286delC frameshift_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576111 p.Ala255Gly missense_variant 0.22
mshA 576114 p.Arg256Pro missense_variant 0.33
ccsA 619958 p.Val23Ala missense_variant 0.22
ccsA 620274 c.384G>T synonymous_variant 0.22
ccsA 620341 p.Val151Leu missense_variant 0.15
rpoB 759715 c.-92G>T upstream_gene_variant 0.33
rpoB 760937 c.1131G>A synonymous_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.25
rpoB 761749 p.Ser648* stop_gained 0.14
rpoB 761814 p.Ala670Pro missense_variant 0.2
rpoB 762280 p.Glu825Gly missense_variant 0.14
rpoC 764877 p.Thr503Asn missense_variant 0.13
rpoC 765058 p.Asn563Lys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775741 c.2740C>T synonymous_variant 0.14
mmpL5 775747 p.Met912Leu missense_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.18
mmpL5 777164 c.1317C>T synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781483 c.-77C>T upstream_gene_variant 0.12
fbiC 1303109 p.Ala60Glu missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305105 c.2175G>T synonymous_variant 0.18
embR 1417422 c.-75C>A upstream_gene_variant 0.13
embR 1417479 c.-132G>A upstream_gene_variant 0.13
embR 1417484 c.-137C>A upstream_gene_variant 0.13
atpE 1460868 c.-177A>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472485 n.640G>T non_coding_transcript_exon_variant 0.17
rrl 1473714 n.57C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673167 c.-273G>T upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
fabG1 1673986 p.Pro183Ser missense_variant 0.13
inhA 1674811 p.Gly204Ser missense_variant 0.15
tlyA 1917898 c.-42T>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918249 p.Gly104Ser missense_variant 0.14
ndh 2102558 p.Ser162Ile missense_variant 0.33
ndh 2102625 p.Ser140Thr missense_variant 0.14
ndh 2102632 c.411C>A synonymous_variant 0.14
ndh 2102638 c.405A>G synonymous_variant 0.14
ndh 2102649 p.Ala132Ser missense_variant 0.14
ndh 2102701 p.Ser114Arg missense_variant 0.14
katG 2154928 p.Arg395Pro missense_variant 0.17
katG 2154993 c.1119C>A synonymous_variant 0.15
PPE35 2167745 p.Thr956Arg missense_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.72
Rv1979c 2221735 p.Arg477Gln missense_variant 0.13
Rv1979c 2222093 p.Ser358Pro missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.33
kasA 2518609 p.Met165Ile missense_variant 0.29
kasA 2518809 p.Lys232Arg missense_variant 0.24
kasA 2518864 c.750G>C synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.4
kasA 2519143 c.1029G>C synonymous_variant 0.4
ahpC 2726556 p.Ala122Thr missense_variant 0.12
pepQ 2859766 p.Val218Ala missense_variant 0.18
thyX 3067340 c.606G>A synonymous_variant 0.14
ald 3087166 p.Ala116Gly missense_variant 0.22
fprA 3474435 c.429C>T synonymous_variant 0.14
fprA 3474869 p.Val288Ala missense_variant 0.15
fprA 3475221 p.Gln405His missense_variant 0.14
Rv3236c 3612577 p.Glu180Asp missense_variant 0.14
Rv3236c 3612873 p.Phe82Leu missense_variant 0.17
Rv3236c 3613192 c.-76G>A upstream_gene_variant 0.14
fbiB 3641708 c.174C>T synonymous_variant 0.13
alr 3840392 p.Met343Ile missense_variant 0.12
alr 3840463 c.958C>A synonymous_variant 0.14
rpoA 3878492 p.Arg6Ser missense_variant 0.14
clpC1 4039594 p.Arg371Gly missense_variant 0.18
clpC1 4039602 p.Ala368Val missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.13
clpC1 4039654 p.Thr351Ser missense_variant 0.14
embC 4240357 c.495C>A synonymous_variant 0.15
embC 4240617 p.Asp252Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242825 p.Gly988Ala missense_variant 0.12
embA 4244667 p.Val479Leu missense_variant 0.17
embA 4244689 p.Lys486Thr missense_variant 0.17
embA 4245295 p.Thr688Lys missense_variant 0.14
embB 4245905 c.-609C>A upstream_gene_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.46
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246747 p.Asp78Glu missense_variant 0.12
embB 4248534 p.Ala674Asp missense_variant 0.2
aftB 4268832 p.Val2Ala missense_variant 0.2
aftB 4268858 c.-22G>T upstream_gene_variant 0.15
ubiA 4269174 p.Phe220Leu missense_variant 0.25
ubiA 4269345 c.487_488delGC frameshift_variant 0.2
aftB 4269768 c.-932C>G upstream_gene_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.22
ethR 4326964 c.-585G>A upstream_gene_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.25
ethR 4327738 p.Tyr64His missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0