TB-Profiler result

Run: ERR2229123
Summary

Run ID: ERR2229123

Sample name:

Date: 31-03-2023 16:42:52

Number of reads: 1072460

Percentage reads mapped: 99.36

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 0.22
mshA 576450 c.1105dupG frameshift_variant 0.15
ccsA 620290 p.Tyr134His missense_variant 0.12
ccsA 620309 c.421delC frameshift_variant 0.14
ccsA 620777 p.Asn296Ile missense_variant 0.12
rpoB 759791 c.-16G>T upstream_gene_variant 0.12
rpoC 764214 p.Arg282Leu missense_variant 0.17
rpoC 764320 c.951C>A synonymous_variant 0.12
rpoC 765274 c.1905G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778662 p.Asp82Tyr missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305138 p.Phe736Leu missense_variant 0.15
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
rpsA 1834357 c.816T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102719 p.Tyr108* stop_gained 0.12
ndh 2103111 c.-69G>T upstream_gene_variant 0.12
PPE35 2167965 c.2646_2647delAG frameshift_variant 0.12
PPE35 2167973 c.2640A>G synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.48
Rv1979c 2222969 p.Ala66Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.24
eis 2715399 c.-67T>C upstream_gene_variant 0.14
ahpC 2726298 p.Thr36Ala missense_variant 0.11
folC 2746646 p.Gln318Arg missense_variant 0.11
pepQ 2859453 c.966G>C synonymous_variant 0.1
pepQ 2859457 p.Val321Ala missense_variant 0.11
pepQ 2860048 c.370delG frameshift_variant 0.15
Rv2752c 3064891 p.Gly434Asp missense_variant 0.18
thyX 3067340 c.606G>A synonymous_variant 0.18
ald 3087842 p.Lys341Asn missense_variant 0.13
whiB7 3568488 c.191delG frameshift_variant 0.11
Rv3236c 3612417 p.Glu234* stop_gained 0.4
Rv3236c 3612870 p.Ala83Thr missense_variant 0.12
fbiB 3641916 p.Ser128Gly missense_variant 0.12
rpoA 3878553 c.-46C>T upstream_gene_variant 0.25
clpC1 4039839 p.Leu289Pro missense_variant 0.12
clpC1 4040396 c.309C>T synonymous_variant 0.13
embC 4241468 p.Ala536Thr missense_variant 0.15
embC 4241761 c.1899G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243503 p.Ser91Thr missense_variant 0.12
embB 4245704 c.-810G>C upstream_gene_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.7
embB 4246556 p.Ala15Pro missense_variant 0.7
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4247695 c.1182G>C synonymous_variant 0.13
embB 4247699 p.Met396Leu missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0