TB-Profiler result

Run: SRR14781887

Summary

Run ID: SRR14781887

Sample name:

Date: 03-04-2023 11:03:29

Number of reads: 2781334

Percentage reads mapped: 96.92

Strain: lineage4.2.1

Drug-resistance: MDR-TB


Download CSV Download TXT Download PDF Download JSON
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247402 p.Ser297Ala missense_variant 1.0 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
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576482 p.Val379Leu missense_variant 0.19
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoC 764817 p.Val483Gly 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 1472544 n.699C>T non_coding_transcript_exon_variant 0.11
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472560 n.715G>T non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.13
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.28
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.24
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472677 n.833_834delTT non_coding_transcript_exon_variant 0.19
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.18
rrs 1472683 n.839_842delGGGA non_coding_transcript_exon_variant 0.18
rrs 1472690 n.845C>G non_coding_transcript_exon_variant 0.18
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472726 n.881G>A non_coding_transcript_exon_variant 0.18
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.17
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.15
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.14
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.26
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.26
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.26
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.3
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.23
rrl 1476518 n.2861G>A non_coding_transcript_exon_variant 0.23
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.23
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.23
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.24
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.23
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.17
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 0.98
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_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
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0