TB-Profiler result

Run: SRR4035816
Summary

Run ID: SRR4035816

Sample name:

Date: 04-04-2023 07:18:50

Number of reads: 1503735

Percentage reads mapped: 99.53

Strain: lineage4.1.2

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
lineage4.1.2 Euro-American T;H 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
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 5479 c.240C>T synonymous_variant 0.14
gyrB 6796 p.Ile519Met missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7937 c.636A>G synonymous_variant 0.12
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8489 c.1188A>G synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491266 p.Ile162Phe missense_variant 0.18
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 0.96
rpoC 762971 c.-399G>A upstream_gene_variant 0.13
rpoB 763147 p.Ser1114Leu missense_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765132 p.Leu588Pro missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765918 p.Phe850Ser missense_variant 0.1
rpoC 767241 p.Gln1291Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775757 c.2724C>A synonymous_variant 0.12
mmpL5 776326 p.Ile719Val missense_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 0.94
mmpS5 778793 p.Leu38Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417237 c.111T>C synonymous_variant 0.12
atpE 1461137 c.93C>A synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472564 n.719A>G non_coding_transcript_exon_variant 0.25
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.18
rrs 1472901 n.1056T>A non_coding_transcript_exon_variant 0.18
rrs 1472935 n.1090G>A non_coding_transcript_exon_variant 0.2
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.17
rrl 1475626 n.1969T>A non_coding_transcript_exon_variant 0.13
rrl 1475634 n.1977G>A non_coding_transcript_exon_variant 0.14
inhA 1674845 c.646delC frameshift_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918336 p.Arg133Gly missense_variant 0.13
tlyA 1918342 p.Asn135Tyr missense_variant 0.15
katG 2155742 p.Gly124Arg missense_variant 0.12
PPE35 2168095 p.Asn840Asp missense_variant 0.12
Rv1979c 2221844 p.Arg441Trp missense_variant 0.15
Rv1979c 2222232 c.933G>A synonymous_variant 0.13
Rv1979c 2222800 p.Phe122Tyr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519053 c.939G>C synonymous_variant 0.11
kasA 2519062 c.948T>C synonymous_variant 0.11
ahpC 2726037 c.-156G>A upstream_gene_variant 0.18
folC 2747461 c.138C>T synonymous_variant 0.17
folC 2747490 p.Arg37Ser missense_variant 0.13
ribD 2986850 c.12T>C synonymous_variant 0.12
ribD 2986921 c.88delC frameshift_variant 0.14
Rv2752c 3065929 p.Gly88Ala missense_variant 0.11
thyX 3067869 p.Thr26Ser missense_variant 0.14
thyX 3067880 c.66C>T synonymous_variant 0.15
thyX 3068068 c.-123C>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086970 p.Lys51Glu missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.93
Rv3236c 3612278 p.Leu280Pro missense_variant 0.11
Rv3236c 3612411 p.Leu236Val missense_variant 0.12
Rv3236c 3612704 p.Glu138Ala missense_variant 0.11
fbiB 3640788 c.-747T>G upstream_gene_variant 0.14
embC 4239806 c.-57C>A upstream_gene_variant 0.13
embC 4240583 p.Thr241Ala missense_variant 0.13
embC 4240597 c.735G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268452 p.Pro129Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407852 c.351G>A synonymous_variant 0.14
gid 4408467 c.-265A>T upstream_gene_variant 0.22