TB-Profiler result

Run: ERR2229056

Summary

Run ID: ERR2229056

Sample name:

Date: 31-03-2023 16:33:38

Number of reads: 759705

Percentage reads mapped: 99.38

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
gyrA 9271 p.Asp657Gly missense_variant 0.15
mshA 576482 p.Val379Leu missense_variant 0.2
rpoC 766752 p.Arg1128Leu missense_variant 0.12
rpoC 767114 p.Lys1249Glu missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781910 c.353dupG frameshift_variant 0.2
rplC 801004 c.196C>T synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304709 c.1779C>G synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474339 n.682C>A non_coding_transcript_exon_variant 0.18
rrl 1474663 n.1006C>A non_coding_transcript_exon_variant 0.12
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 0.15
rrl 1474927 n.1270T>A non_coding_transcript_exon_variant 0.17
inhA 1674671 p.Ala157Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101781 p.Phe421Tyr missense_variant 0.14
katG 2154582 c.1530C>T synonymous_variant 0.25
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170189 p.Glu142Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518867 c.753G>A synonymous_variant 0.13
kasA 2518879 c.765A>G synonymous_variant 0.14
eis 2715059 p.Arg92Cys missense_variant 0.14
ahpC 2725969 c.-224C>G upstream_gene_variant 0.14
folC 2746591 c.1008C>T synonymous_variant 0.4
thyX 3067418 c.528C>A synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 0.11
fprA 3474969 c.963G>T synonymous_variant 0.29
fbiB 3642167 c.633G>C synonymous_variant 0.14
alr 3840786 p.Ala212Val missense_variant 0.11
clpC1 4038773 p.Asp644Glu missense_variant 0.14
clpC1 4038776 p.Glu643Asp missense_variant 0.14
clpC1 4038782 c.1923G>C synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.13
panD 4044023 c.259C>T synonymous_variant 0.18
panD 4044209 p.Ser25Ala missense_variant 0.14
embC 4240597 c.735G>T synonymous_variant 0.15
embC 4241551 c.1689A>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242919 c.-314A>G upstream_gene_variant 0.13
embA 4242979 c.-254G>T upstream_gene_variant 0.14
embA 4245792 p.Ser854Pro missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246747 p.Asp78Glu missense_variant 0.18
embB 4247260 c.747C>A synonymous_variant 0.2
embB 4248360 p.Pro616Leu missense_variant 0.13
aftB 4268923 c.-87C>A upstream_gene_variant 0.13
ubiA 4269638 p.Ala66Ser missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0