TB-Profiler result

Run: ERR2229484
Summary

Run ID: ERR2229484

Sample name:

Date: 31-03-2023 17:14:51

Number of reads: 519673

Percentage reads mapped: 99.31

Strain: lineage4

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
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 5470 c.231C>T synonymous_variant 0.25
gyrB 6506 p.Ala423Ser missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620169 c.279G>A synonymous_variant 0.4
rpoB 759757 c.-50G>A upstream_gene_variant 0.15
rpoB 759975 p.Trp57Arg missense_variant 0.12
rpoB 760019 c.213G>T synonymous_variant 0.13
rpoB 761847 p.Cys681Arg missense_variant 0.17
rpoB 762234 p.Pro810Ser missense_variant 0.25
rpoC 765807 p.Gln813Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.2
mmpL5 775741 c.2740C>T synonymous_variant 0.2
mmpL5 775742 c.2739C>T synonymous_variant 0.2
mmpL5 775747 p.Met912Leu missense_variant 0.18
mmpL5 776034 p.Phe816Tyr missense_variant 0.33
mmpL5 777488 p.Tyr331* stop_gained 0.17
mmpL5 777525 p.Gly319Val missense_variant 0.2
mmpR5 778406 c.-584G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800878 p.Val24Leu missense_variant 0.29
fbiC 1303558 p.Ser210Ala missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303979 p.Gly350Val missense_variant 0.29
fbiC 1304706 p.His592Gln missense_variant 0.33
fbiC 1304869 c.1939C>T synonymous_variant 0.17
fbiC 1305484 c.2557delC frameshift_variant 0.14
Rv1258c 1406123 c.1218G>T synonymous_variant 0.33
Rv1258c 1406603 c.738G>C synonymous_variant 0.14
atpE 1461069 p.Ala9Ser missense_variant 0.4
atpE 1461093 p.Met17Leu missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475901 n.2244C>A non_coding_transcript_exon_variant 0.22
inhA 1674567 c.366C>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102024 c.1018delG frameshift_variant 0.17
katG 2154405 c.1707G>T synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2168140 p.Ala825Thr missense_variant 0.12
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169033 p.Phe527Ser missense_variant 0.12
PPE35 2169322 c.1291T>C synonymous_variant 0.14
PPE35 2169323 c.1290C>G synonymous_variant 0.14
PPE35 2169326 c.1287C>T synonymous_variant 0.14
PPE35 2169337 p.Asp426His missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.7
PPE35 2170249 p.Ile122Val missense_variant 0.12
PPE35 2170269 p.Ser115Tyr missense_variant 0.14
PPE35 2170371 p.Thr81Val missense_variant 0.14
PPE35 2170415 c.198A>G synonymous_variant 0.17
PPE35 2170527 p.Ser29Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289666 c.-425C>T upstream_gene_variant 0.18
kasA 2518879 c.765A>G synonymous_variant 0.22
kasA 2518882 c.768C>A synonymous_variant 0.22
pepQ 2860304 p.Ser39Pro missense_variant 0.15
Rv2752c 3065324 p.Ala290Ser missense_variant 0.12
fbiD 3339155 p.Ile13Ser missense_variant 0.12
fprA 3473981 c.-26G>A upstream_gene_variant 0.18
fbiA 3641467 p.Leu309Met missense_variant 0.14
alr 3840877 p.Ala182Ser missense_variant 0.12
alr 3841263 p.Arg53Leu missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.31
clpC1 4038899 c.1806C>T synonymous_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040678 c.27C>A synonymous_variant 0.15
clpC1 4040765 c.-61G>T upstream_gene_variant 0.14
panD 4044335 c.-54C>A upstream_gene_variant 0.33
embC 4241459 p.Arg533Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244116 p.Arg295Leu missense_variant 0.18
embA 4244451 p.Pro407Thr missense_variant 0.25
embA 4244852 c.1620G>T synonymous_variant 0.25
embA 4245017 p.Ile595Met missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4247103 p.Pro197Leu missense_variant 0.29
embB 4247230 c.717G>T synonymous_variant 0.29
embB 4248751 c.2238C>A synonymous_variant 0.2
aftB 4267308 p.Leu510Pro missense_variant 0.14
aftB 4268536 p.Gly101Trp missense_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.4
ethA 4328283 c.-810G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>A upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0