TB-Profiler result

Run: SRR4033284
Summary

Run ID: SRR4033284

Sample name:

Date: 04-04-2023 05:58:06

Number of reads: 631450

Percentage reads mapped: 99.79

Strain: lineage4.8.1

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
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
gyrB 5264 p.Gln9Lys missense_variant 0.14
gyrB 7185 p.Ser649Tyr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8210 p.Glu303Asp missense_variant 0.12
fgd1 490928 p.Gly49Val missense_variant 0.13
fgd1 491520 c.738C>A synonymous_variant 0.17
mshA 576223 c.876G>T synonymous_variant 0.14
rpoB 761610 p.Gly602Trp missense_variant 0.22
rpoC 764375 p.Ala336Ser missense_variant 0.13
rpoC 764921 c.1554delA frameshift_variant 0.22
rpoC 766381 c.3012C>T synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777446 c.1034delT frameshift_variant 0.2
mmpR5 779085 p.Leu32Phe missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303371 c.441C>A synonymous_variant 0.17
fbiC 1305262 p.His778Asn missense_variant 0.15
embR 1416857 p.Thr164Lys missense_variant 0.14
atpE 1460860 c.-185C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472010 n.165C>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475227 n.1570T>G non_coding_transcript_exon_variant 0.29
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.22
rrl 1476379 n.2722G>T non_coding_transcript_exon_variant 0.17
fabG1 1673521 p.Gly28Arg missense_variant 0.29
fabG1 1673720 p.Asp94Gly missense_variant 0.18
inhA 1674859 c.659delA frameshift_variant 0.29
rpsA 1834156 c.615C>T synonymous_variant 0.15
rpsA 1834486 p.Glu315Asp missense_variant 0.25
rpsA 1834651 c.1110C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 c.936delC frameshift_variant 0.5
katG 2154464 p.Ala550Thr missense_variant 0.2
katG 2154579 c.1533C>T synonymous_variant 0.2
katG 2155992 c.120C>A synonymous_variant 0.18
katG 2156055 c.57C>A synonymous_variant 0.15
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168402 c.2211A>G synonymous_variant 0.11
PPE35 2168641 p.Ile658Val missense_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.23
PPE35 2170104 p.Leu170Pro missense_variant 0.14
Rv1979c 2222278 p.Gly296Val missense_variant 0.22
Rv1979c 2222291 p.Ala292Thr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223306 c.-142T>C upstream_gene_variant 0.22
pncA 2289086 c.156C>A synonymous_variant 0.14
kasA 2518517 c.403C>A synonymous_variant 0.17
eis 2715400 c.-68C>A upstream_gene_variant 0.2
ahpC 2726159 c.-34A>G upstream_gene_variant 0.12
folC 2747454 c.145C>A synonymous_variant 0.14
pepQ 2859759 c.660C>A synonymous_variant 0.12
pepQ 2859926 p.Pro165Ser missense_variant 0.14
Rv2752c 3065521 p.Arg224Gln missense_variant 0.22
thyX 3067221 p.Ala242Val missense_variant 0.2
thyX 3067330 p.Val206Met missense_variant 0.22
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
Rv3083 3448409 c.-95G>T upstream_gene_variant 0.29
fprA 3474551 p.Ala182Asp missense_variant 0.67
fprA 3474798 c.792C>T synonymous_variant 0.18
Rv3236c 3612617 p.Pro167Leu missense_variant 0.4
fbiB 3642874 p.Leu447Arg missense_variant 1.0
alr 3840618 p.Asp268Gly missense_variant 0.13
rpoA 3877696 p.Thr271Ile missense_variant 0.15
ddn 3987111 p.Leu90Ile missense_variant 0.2
clpC1 4038214 p.Asp831Tyr missense_variant 0.33
clpC1 4040709 c.-5C>A upstream_gene_variant 0.14
panD 4044107 p.Ala59Ser missense_variant 0.11
embC 4240447 c.585G>A synonymous_variant 0.12
embC 4241148 p.Cys429Tyr missense_variant 0.17
embC 4241200 c.1338C>A synonymous_variant 0.13
embC 4241702 p.Arg614Ser missense_variant 0.14
embA 4242598 c.-635T>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247155 c.642G>A synonymous_variant 0.15
embB 4249618 c.3105C>A synonymous_variant 0.25
aftB 4267622 c.1215G>T synonymous_variant 0.4
aftB 4268730 p.Arg36Leu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-78delA upstream_gene_variant 0.25
whiB6 4338607 c.-86C>A upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0