TB-Profiler result

Run: SRR833022
Summary

Run ID: SRR833022

Sample name:

Date: 04-04-2023 20:56:25

Number of reads: 519429

Percentage reads mapped: 84.86

Strain: lineage4

Drug-resistance: HR-TB

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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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2154538 p.Gln525Pro missense_variant 0.25 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288699 p.Glu181Asp missense_variant 0.4 pyrazinamide
pncA 2288790 p.Leu151Ser missense_variant 0.18 pyrazinamide
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 9106 p.Phe602Ser missense_variant 0.2
gyrA 9211 c.1914_1917dupCGAC frameshift_variant 0.18
fgd1 491790 c.1008C>T synonymous_variant 0.14
mshA 576049 c.702A>C synonymous_variant 0.2
ccsA 619885 c.-6C>A upstream_gene_variant 0.4
rpoB 759736 c.-71G>C upstream_gene_variant 0.15
rpoB 759891 p.Ala29Pro missense_variant 0.18
rpoB 761484 p.Gly560Ser missense_variant 0.33
rpoB 761532 p.Ser576Pro missense_variant 0.33
rpoC 763508 c.143_154delGCGAGAAGATCT disruptive_inframe_deletion 0.2
rpoC 764812 c.1443C>A synonymous_variant 0.2
rpoC 765009 p.Leu547Trp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776140 p.Ile781Val missense_variant 0.13
mmpL5 777664 p.Ala273Ser missense_variant 0.33
mmpL5 777665 c.816G>A synonymous_variant 0.33
mmpL5 777808 p.Ser225Ala missense_variant 0.2
mmpS5 778641 p.Ser89Ala missense_variant 0.33
mmpS5 778754 p.Phe51Cys missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781499 c.-61A>G upstream_gene_variant 0.5
rpsL 781551 c.-9A>G upstream_gene_variant 0.2
rpsL 781791 p.Ser78Pro missense_variant 0.18
rplC 801396 c.588T>C synonymous_variant 0.15
fbiC 1302772 c.-159T>C upstream_gene_variant 0.5
fbiC 1302787 c.-144T>A upstream_gene_variant 0.33
fbiC 1303644 c.714G>C synonymous_variant 0.67
fbiC 1303645 p.Ala239Pro missense_variant 0.67
fbiC 1304888 p.Leu653Pro missense_variant 0.29
fbiC 1305282 p.Ile784Met missense_variant 0.22
embR 1416716 p.Leu211Arg missense_variant 0.43
embR 1416988 p.Thr120Ala missense_variant 1.0
embR 1417447 c.-100A>C upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474065 n.408C>T non_coding_transcript_exon_variant 0.14
rrl 1476683 n.3026T>G non_coding_transcript_exon_variant 0.2
fabG1 1673651 p.Ala71Val missense_variant 0.25
fabG1 1673653 p.Phe72Val missense_variant 0.22
inhA 1674383 p.Leu61Pro missense_variant 0.4
tlyA 1918672 p.Thr245Pro missense_variant 0.2
ndh 2102486 p.Ala186Gly missense_variant 0.18
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155414 p.Glu233Ala missense_variant 0.29
PPE35 2168178 p.Pro812Arg missense_variant 0.12
PPE35 2168346 p.Val756Gly missense_variant 0.14
PPE35 2168349 p.Gly755Ala missense_variant 0.15
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169862 p.Asn251His missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518516 c.402C>G synonymous_variant 0.18
kasA 2519313 p.Asn400Ser missense_variant 0.4
eis 2714216 p.Asn373His missense_variant 0.29
ahpC 2726428 p.Asp79Gly missense_variant 0.2
ahpC 2726431 p.Ala80Val missense_variant 0.2
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
thyX 3067477 p.Gln157Lys missense_variant 1.0
thyX 3067479 p.Asp156Gly missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.33
thyA 3074641 c.-170C>T upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087141 c.322T>C synonymous_variant 0.18
fbiD 3339182 p.Ala22Asp missense_variant 0.67
fbiD 3339287 p.Arg57Leu missense_variant 1.0
fbiD 3339391 p.Leu92Trp missense_variant 0.67
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448895 p.Tyr131Ser missense_variant 0.67
Rv3083 3449809 p.Phe436Val missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474590 p.Val195Gly missense_variant 0.22
fprA 3474865 c.860dupT frameshift_variant 0.33
fprA 3474914 p.Ala303Val missense_variant 1.0
Rv3236c 3613137 c.-21T>C upstream_gene_variant 0.14
fbiA 3640907 p.Gly122Ala missense_variant 0.22
fbiB 3641948 c.414G>A synonymous_variant 1.0
alr 3840687 p.Asp245Ala missense_variant 0.18
panD 4044400 c.-119G>A upstream_gene_variant 0.15
embC 4241384 p.Pro508Thr missense_variant 0.2
embC 4242296 p.Asp812Asn missense_variant 0.5
embA 4244911 p.Leu560Pro missense_variant 1.0
embA 4244913 p.Leu561Val missense_variant 1.0
embA 4245112 p.Val627Ala missense_variant 0.17
embB 4249515 p.Leu1001Pro missense_variant 0.29
aftB 4267513 c.1323delG frameshift_variant 0.5
aftB 4268619 p.Val73Ala missense_variant 0.29
ubiA 4269242 p.Leu198Met missense_variant 0.18
ubiA 4269308 p.Phe176Leu missense_variant 1.0
ubiA 4269452 p.Met128Leu missense_variant 0.21
ubiA 4269871 c.-39_-38insA upstream_gene_variant 1.0
ethA 4326792 p.Trp228Arg missense_variant 0.4
ethR 4328075 p.Asn176Thr missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0