TB-Profiler result

Run: SRR21677893
Summary

Run ID: SRR21677893

Sample name:

Date: 04-04-2023 02:49:59

Number of reads: 865987

Percentage reads mapped: 89.67

Strain: lineage4.1.1.3

Drug-resistance: Sensitive

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
lineage4.1 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
gyrB 5478 p.Asp80Gly missense_variant 0.17
gyrB 6810 p.Tyr524Phe missense_variant 0.17
gyrA 7210 c.-92C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8702 c.1401C>T synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575663 p.Gly106Arg missense_variant 0.11
ccsA 620451 c.561G>A synonymous_variant 0.13
rpoB 761302 p.Arg499Gln missense_variant 0.13
rpoB 762731 p.Gln975His missense_variant 0.15
rpoC 764598 p.Gln410Pro missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766735 c.3366G>T synonymous_variant 0.11
mmpL5 775637 p.Ile948Val missense_variant 0.11
mmpL5 775696 p.Ile929Phe missense_variant 0.11
mmpL5 777407 c.1074C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 801241 p.His145Asn missense_variant 0.11
rplC 801246 c.438C>A synonymous_variant 0.11
Rv1258c 1407180 p.Pro54Gln missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
fabG1 1674164 p.Gly242Asp missense_variant 0.11
inhA 1674751 p.Val184Leu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155813 p.Pro100Arg missense_variant 0.11
PPE35 2167804 p.Gly937Cys missense_variant 0.22
PPE35 2167924 p.Gly897Cys missense_variant 0.14
PPE35 2168836 p.Pro593Thr missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289426 c.-185G>C upstream_gene_variant 0.14
pncA 2289451 c.-210G>C upstream_gene_variant 0.12
pncA 2289493 c.-252T>G upstream_gene_variant 0.12
pncA 2289501 c.-260G>C upstream_gene_variant 0.11
pncA 2290063 c.-822G>A upstream_gene_variant 0.13
pncA 2290095 c.-854C>T upstream_gene_variant 0.13
kasA 2518984 c.870G>T synonymous_variant 0.12
kasA 2519003 p.Leu297Met missense_variant 0.11
kasA 2519178 p.Ser355Leu missense_variant 0.17
eis 2714954 p.Gly127Ser missense_variant 0.12
eis 2715062 p.His91Asn missense_variant 0.14
eis 2715541 c.-222_-210delCCATGGGACCGGT upstream_gene_variant 0.14
folC 2746250 c.1346_1348delACG disruptive_inframe_deletion 0.11
ribD 2987262 p.Val142Met missense_variant 0.12
Rv2752c 3064645 c.1546delG frameshift_variant 0.17
Rv2752c 3064918 p.Asn425Ser missense_variant 0.1
Rv2752c 3065952 c.240C>T synonymous_variant 0.12
thyX 3068116 c.-173_-172delCG upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087570 p.Ser251Thr missense_variant 0.11
fbiD 3339309 c.192C>A synonymous_variant 0.11
fprA 3473839 c.-168G>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474968 p.Ser321Leu missense_variant 0.11
Rv3236c 3613097 p.Leu7Pro missense_variant 0.1
Rv3236c 3613151 c.-35C>T upstream_gene_variant 0.14
fbiB 3642645 p.Thr371Ser missense_variant 0.25
fbiB 3642691 p.Val386Ala missense_variant 0.25
rpoA 3878082 c.426T>A synonymous_variant 0.11
rpoA 3878419 p.Phe30Ser missense_variant 0.12
rpoA 3878489 c.17_18delGC frameshift_variant 0.11
panD 4044445 c.-164G>T upstream_gene_variant 0.12
embC 4239885 p.Pro8Arg missense_variant 0.11
embC 4240962 c.1101_1109delGGGGCACGC disruptive_inframe_deletion 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243268 p.Ile12Met missense_variant 0.12
embA 4243357 p.Thr42Asn missense_variant 0.12
embA 4243659 p.Ala143Thr missense_variant 0.12
embA 4243729 p.Lys166Arg missense_variant 0.15
embA 4244860 p.Gly543Glu missense_variant 1.0
embA 4244886 p.Leu552Met missense_variant 0.14
embA 4245691 p.Gly820Val missense_variant 0.11
embA 4245717 p.Pro829Thr missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4248604 c.2091G>T synonymous_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249483 c.2972delG frameshift_variant 0.13
aftB 4266973 p.Gly622Cys missense_variant 0.12
aftB 4267652 p.Met395Ile missense_variant 0.12
ubiA 4269377 p.Val153Leu missense_variant 0.11
ethR 4328089 p.Arg181Trp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0