TB-Profiler result

Run: ERR2229442
Summary

Run ID: ERR2229442

Sample name:

Date: 31-03-2023 17:11:52

Number of reads: 903572

Percentage reads mapped: 98.34

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2154735 c.1376delA frameshift_variant 0.12 isoniazid
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 8699 c.1398A>G synonymous_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.17
ccsA 620864 c.974G>T stop_lost&splice_region_variant 0.14
rpoB 761516 c.1710G>C synonymous_variant 0.12
rpoB 761570 c.1764T>C synonymous_variant 0.1
rpoB 761600 c.1794T>C synonymous_variant 0.11
rpoB 761806 p.Arg667Leu missense_variant 0.15
rpoC 763528 c.159G>C synonymous_variant 0.1
rpoC 763531 c.162G>C synonymous_variant 0.1
rpoC 763534 c.165T>C synonymous_variant 0.1
rpoC 763546 c.177A>G synonymous_variant 0.11
rpoC 763550 p.Tyr61Ala missense_variant 0.11
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763594 c.225C>T synonymous_variant 0.14
rpoC 764485 c.1116G>C synonymous_variant 0.12
rpoC 764497 c.1128A>G synonymous_variant 0.11
rpoC 764498 p.Ser377Ala missense_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.13
rpoC 764536 c.1167G>T synonymous_variant 0.15
rpoC 764539 c.1170C>G synonymous_variant 0.15
rpoC 764542 c.1173C>G synonymous_variant 0.14
rpoC 764609 p.Arg414Trp missense_variant 0.15
rpoC 766939 c.3570C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Val missense_variant 0.12
mmpL5 775817 c.2664T>C synonymous_variant 0.12
mmpL5 777602 p.Gln293His missense_variant 0.13
mmpS5 778812 p.Phe32Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801030 c.222C>T synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304935 p.Ala669Ser missense_variant 0.2
embR 1416841 c.507C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.17
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.15
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.19
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.19
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.2
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.33
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.31
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.35
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.31
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.28
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.27
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.28
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.2
rrl 1475688 n.2031G>A non_coding_transcript_exon_variant 0.15
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.15
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.16
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.23
fabG1 1673359 c.-81T>C upstream_gene_variant 0.23
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
fabG1 1673533 p.Ala32Thr missense_variant 0.12
rpsA 1833742 c.201A>G synonymous_variant 0.15
rpsA 1833763 c.222C>G synonymous_variant 0.13
rpsA 1833769 c.228C>G synonymous_variant 0.13
rpsA 1833770 p.Asn77Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103215 c.-173C>A upstream_gene_variant 0.15
katG 2154248 p.Pro622Thr missense_variant 0.17
katG 2154900 p.Leu404Phe missense_variant 0.17
PPE35 2167878 p.Ser912Asn missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519153 p.Ile347Val missense_variant 0.14
pepQ 2859971 p.Ala150Ser missense_variant 0.15
ribD 2986872 c.38dupC frameshift_variant 0.12
ribD 2987114 c.276C>A synonymous_variant 0.13
ribD 2987221 p.Arg128His missense_variant 0.12
thyA 3074580 c.-109T>C upstream_gene_variant 0.13
fbiD 3339369 c.252A>T synonymous_variant 0.18
fbiD 3339704 p.Thr196Lys missense_variant 0.12
fprA 3475293 p.Phe429Leu missense_variant 0.18
Rv3236c 3612093 p.Gly342Trp missense_variant 0.12
fbiB 3642577 p.Val348Ala missense_variant 0.17
alr 3840200 c.1220delA frameshift_variant 0.12
alr 3840470 c.951C>A synonymous_variant 0.12
alr 3841014 p.Arg136Pro missense_variant 0.15
clpC1 4038314 c.2391T>A synonymous_variant 0.13
panD 4043900 p.Ala128Thr missense_variant 0.17
panD 4044271 p.Thr4Met missense_variant 0.14
panD 4044430 c.-149C>T upstream_gene_variant 0.2
embC 4241223 p.Gly454Val missense_variant 0.12
embC 4241356 p.Gln498His missense_variant 0.14
embC 4241772 p.Val637Ala missense_variant 0.22
embC 4242105 p.Thr748Ile missense_variant 0.17
embC 4242552 p.Arg897Gln missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242759 p.Pro966Gln missense_variant 0.15
embC 4242791 p.Ala977Pro missense_variant 0.2
embA 4243667 c.435C>A synonymous_variant 0.15
embA 4245600 p.Pro790Ser missense_variant 0.5
embB 4245644 c.-870C>A upstream_gene_variant 0.18
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.2
embA 4245844 p.Val871Glu missense_variant 0.2
embA 4245846 p.Ser872Thr missense_variant 0.22
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.29
embB 4246760 p.Val83Met missense_variant 0.12
embB 4247026 c.513G>C synonymous_variant 0.25
embB 4249750 c.3237G>A synonymous_variant 0.18
aftB 4268281 c.556C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0