TB-Profiler result

Run: SRR5341306
Summary

Run ID: SRR5341306

Sample name:

Date: 04-04-2023 10:14:01

Number of reads: 6023637

Percentage reads mapped: 89.28

Strain: lineage4.4

Drug-resistance: Pre-XDR-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
lineage4.4 Euro-American S;T 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
gyrA 7582 p.Asp94Gly missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpoC 765572 p.Asp735Asn missense_variant 1.0 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.76 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.18 streptomycin
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.17
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.13
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.12
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.12
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.12
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.13
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.13
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.11
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.13
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.12
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.14
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.24
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.28
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.21
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.1
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.11
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.11
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.13
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.11
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.1
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.15
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.18
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.18
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.14
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.11
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.12
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.1
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.1
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.1
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.16
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.25
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.25
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.11
rrl 1476108 n.2451T>G non_coding_transcript_exon_variant 0.11
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.11
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.2
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.34
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.26
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153924 p.Lys730Glu missense_variant 1.0
katG 2154226 p.Gly629Ala missense_variant 1.0
PPE35 2170558 p.Ala19Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714523 p.His270Gln missense_variant 0.98
Rv2752c 3065715 c.477T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243324 p.Val31Ala missense_variant 1.0
embB 4247548 c.1035C>T synonymous_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0