TB-Profiler result

Run: SRR4033131
Summary

Run ID: SRR4033131

Sample name:

Date: 04-04-2023 05:50:41

Number of reads: 1078859

Percentage reads mapped: 99.15

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 0.96
lineage4.1.2 Euro-American T;H None 0.94
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 8061 p.Arg254Cys missense_variant 0.97
gyrA 9286 p.Ala662Val missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575755 c.408G>T synonymous_variant 0.17
ccsA 620355 p.Trp155* stop_gained 0.2
ccsA 620382 p.Met164Ile missense_variant 0.18
ccsA 620499 c.609G>T synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761025 p.Thr407Ala missense_variant 0.13
rpoB 763246 c.3442delG frameshift_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 0.96
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765972 p.Ala868Val missense_variant 0.14
rpoC 767180 p.Ala1271Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775761 p.Gly907Asp missense_variant 0.29
mmpL5 777260 c.1221C>A synonymous_variant 0.17
mmpL5 777320 c.1161C>G synonymous_variant 0.86
mmpS5 778545 p.Glu121Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781596 c.37C>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 0.17
embR 1416543 p.Thr269Ala missense_variant 0.15
rrs 1471655 n.-191G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473596 n.-62G>T upstream_gene_variant 0.11
inhA 1674209 p.Gly3Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102070 p.Ala325Ser missense_variant 0.13
ndh 2102115 p.Ser310Pro missense_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.23
Rv1979c 2222334 c.831C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2725954 c.-239C>T upstream_gene_variant 0.12
folC 2746597 c.1002C>A synonymous_variant 0.17
thyX 3067288 p.Ala220Thr missense_variant 0.11
ald 3086653 c.-167C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448726 p.Leu75Ile missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474320 p.Gly105Asp missense_variant 0.22
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiA 3640529 c.-14T>C upstream_gene_variant 0.13
fbiA 3641453 p.Arg304Leu missense_variant 0.4
clpC1 4038306 c.2398delG frameshift_variant 0.14
clpC1 4039458 p.Thr416Ile missense_variant 0.15
clpC1 4039987 p.Glu240* stop_gained 0.12
embC 4242039 p.Ala726Glu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.86
embA 4243340 c.108G>A synonymous_variant 0.18
embA 4243530 p.Thr100Ala missense_variant 0.18
embA 4245699 p.Gly823Trp missense_variant 0.18
embB 4247738 p.Ala409Ser missense_variant 0.13
embB 4247746 c.1233C>A synonymous_variant 0.14
aftB 4268442 p.Arg132His missense_variant 0.11
aftB 4268485 p.Leu118Phe missense_variant 0.13
aftB 4268507 c.330G>A synonymous_variant 0.15
ubiA 4269748 p.Asn29Ser missense_variant 0.2
ethR 4326955 c.-594G>A upstream_gene_variant 0.13
ethA 4327656 c.-183A>C upstream_gene_variant 0.18
ethR 4327975 p.Gln143* stop_gained 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0