TB-Profiler result

Run: SRR6789630
Summary

Run ID: SRR6789630

Sample name:

Date: 04-04-2023 16:04:24

Number of reads: 828823

Percentage reads mapped: 92.01

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491376 p.Lys198Asn missense_variant 0.11
rpoB 763186 p.Leu1127Pro missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777892 p.Gln197* stop_gained 0.15
mmpS5 778514 p.Val131Glu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
fbiC 1302770 c.-161T>C upstream_gene_variant 0.13
fbiC 1302794 c.-137A>G upstream_gene_variant 0.11
fbiC 1305409 c.2481delC frameshift_variant 0.12
Rv1258c 1406644 p.Leu233Met missense_variant 0.15
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.14
Rv1258c 1406946 p.Ala132Gly missense_variant 0.14
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.14
atpE 1460901 c.-143delA upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.15
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.13
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
rpsA 1834849 c.1308C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918007 p.Ala23Asp missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170147 p.Ser156Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288726 c.516G>A synonymous_variant 0.12
folC 2747466 p.Pro45Ser missense_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.11
ribD 2987290 p.Asp151Val missense_variant 0.11
Rv2752c 3065439 c.753C>T synonymous_variant 0.17
thyX 3067422 p.Leu175Pro missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339397 p.Thr94Ser missense_variant 0.18
fbiD 3339541 p.Asp142Asn missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474302 p.Ala99Asp missense_variant 0.17
fbiA 3640439 c.-104C>T upstream_gene_variant 0.12
fbiA 3640450 c.-93T>C upstream_gene_variant 0.11
fbiA 3640546 p.Lys2Glu missense_variant 0.11
fbiB 3642050 c.516G>T synonymous_variant 0.15
clpC1 4040831 c.-128delG upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243396 p.Ile55Thr missense_variant 0.2
embA 4243877 c.645G>A synonymous_variant 0.12
embA 4244007 p.Ala259Thr missense_variant 0.12
embA 4244598 p.Leu456Met missense_variant 0.12
embA 4244625 p.Leu465Met missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4247989 c.1476G>C synonymous_variant 0.1
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269277 p.Phe186Ser missense_variant 0.12
ethR 4327633 p.Ile29Phe missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407626 p.Ala193Thr missense_variant 0.11
gid 4407798 c.405G>T synonymous_variant 1.0