TB-Profiler result

Run: SRR21677856

Summary

Run ID: SRR21677856

Sample name:

Date: 04-04-2023 02:48:33

Number of reads: 418749

Percentage reads mapped: 99.21

Strain: lineage4.8

Drug-resistance: Other


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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
pncA 2288826 p.Val139Ala missense_variant 0.1 pyrazinamide
ethA 4327269 c.204delC frameshift_variant 0.17 ethionamide
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 6728 c.-574C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8063 c.762C>A synonymous_variant 0.12
gyrA 8459 c.1159_1167delCGAGCCCAC conservative_inframe_deletion 0.14
gyrA 9612 p.Asp771His missense_variant 0.11
fgd1 491042 p.Ala87Asp missense_variant 0.12
fgd1 491091 c.309T>A synonymous_variant 0.18
fgd1 491791 c.1009T>C stop_lost&splice_region_variant 0.11
mshA 576036 p.Ala230Val missense_variant 0.14
ccsA 619914 c.24C>T synonymous_variant 0.2
ccsA 620071 p.Pro61Ser missense_variant 0.12
ccsA 620434 p.Gly182Arg missense_variant 0.12
rpoB 762986 p.Gln1060His missense_variant 0.11
rpoB 763050 p.Leu1082Met missense_variant 0.14
rpoB 763069 p.Asp1088Val missense_variant 0.11
rpoB 763095 p.Tyr1097His missense_variant 0.13
rpoC 763136 c.-234C>A upstream_gene_variant 0.12
rpoC 766180 p.Ile937Met missense_variant 0.17
rpoC 766622 c.3253C>A synonymous_variant 0.18
rpoC 767200 c.3831G>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775803 p.Met893Thr missense_variant 0.1
mmpL5 775829 c.2652C>G synonymous_variant 0.15
mmpL5 776393 c.2087delT frameshift_variant 0.18
mmpL5 778149 p.Gln111Arg missense_variant 0.11
mmpL5 779004 c.-524G>A upstream_gene_variant 0.22
mmpS5 779609 c.-704C>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781613 p.Lys18Asn missense_variant 0.15
fbiC 1304161 c.1231C>A synonymous_variant 0.33
fbiC 1304381 p.Ala484Val missense_variant 0.18
fbiC 1304434 p.Ala502Ser missense_variant 0.18
fbiC 1304502 c.1572G>A synonymous_variant 0.15
fbiC 1305434 p.Ala835Glu missense_variant 0.12
Rv1258c 1406370 p.Val324Ala missense_variant 0.22
Rv1258c 1406633 c.708C>T synonymous_variant 0.12
Rv1258c 1407459 c.-119T>C upstream_gene_variant 0.11
Rv1258c 1407495 c.-155C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471869 n.24G>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474157 n.500G>T non_coding_transcript_exon_variant 0.12
rrl 1475840 n.2183G>A non_coding_transcript_exon_variant 0.14
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1674009 p.Met190Ile missense_variant 0.15
rpsA 1833747 p.Ser69Cys missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102068 c.975T>C synonymous_variant 0.14
katG 2153918 p.Met732Leu missense_variant 0.17
katG 2154040 p.Gly691Asp missense_variant 0.15
katG 2154250 p.Ala621Val missense_variant 0.11
katG 2154502 p.Lys537Arg missense_variant 0.1
katG 2155258 p.Gly285Val missense_variant 0.14
PPE35 2168109 p.Thr835Ile missense_variant 0.14
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168305 p.Thr770Ser missense_variant 0.13
PPE35 2170719 c.-107T>A upstream_gene_variant 0.12
Rv1979c 2222969 p.Ala66Thr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289788 c.-547A>T upstream_gene_variant 0.17
pncA 2289883 c.-642C>A upstream_gene_variant 0.2
kasA 2518031 c.-84G>T upstream_gene_variant 0.14
kasA 2518210 c.96G>A synonymous_variant 0.12
kasA 2518324 c.213_214dupCA frameshift_variant 0.18
kasA 2518626 p.Cys171Tyr missense_variant 0.2
ahpC 2726091 c.-102G>A upstream_gene_variant 0.1
folC 2747644 c.-46C>T upstream_gene_variant 0.14
pepQ 2860613 c.-195C>A upstream_gene_variant 0.17
ribD 2987068 p.Leu77His missense_variant 0.13
ribD 2987251 p.Met138Thr missense_variant 0.14
ribD 2987453 c.615T>G synonymous_variant 0.12
Rv2752c 3064907 p.Val429Ile missense_variant 0.18
Rv2752c 3065631 c.561C>A synonymous_variant 0.14
Rv2752c 3065890 p.Pro101Leu missense_variant 0.12
thyX 3067273 p.Ala225Thr missense_variant 0.25
thyX 3067278 p.Ala223Asp missense_variant 0.25
thyA 3073715 c.756delT frameshift_variant 0.15
ald 3087690 p.His291Tyr missense_variant 0.17
ald 3087700 p.Leu294Arg missense_variant 0.13
fbiD 3339143 c.28_35delATCGGCTT frameshift_variant 0.11
fbiD 3339507 c.390G>A synonymous_variant 0.33
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3473822 c.-184delG upstream_gene_variant 0.12
fprA 3473825 c.-182T>C upstream_gene_variant 0.12
fprA 3474446 p.Gly147Asp missense_variant 0.11
Rv3236c 3612733 c.384C>A synonymous_variant 0.2
fbiB 3641106 c.-429C>T upstream_gene_variant 0.18
fbiB 3642187 p.Arg218Leu missense_variant 0.11
fbiB 3642255 p.Phe241Leu missense_variant 0.18
alr 3841254 p.Ala56Asp missense_variant 0.13
rpoA 3878045 p.Ser155Pro missense_variant 0.11
rpoA 3878196 c.311delA frameshift_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039770 p.Leu312His missense_variant 0.13
clpC1 4040041 p.Lys222Glu missense_variant 0.22
clpC1 4040584 p.Gly41Arg missense_variant 0.11
clpC1 4040714 c.-10G>C upstream_gene_variant 0.13
panD 4044390 c.-109T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243038 p.Ala1059Val missense_variant 0.17
embA 4243444 p.Asp71Val missense_variant 0.22
embA 4244329 p.Ala366Val missense_variant 0.22
embA 4244448 p.Ala406Ser missense_variant 0.2
embA 4244843 c.1611G>A synonymous_variant 0.18
embA 4245373 p.Pro714Arg missense_variant 0.13
embA 4245478 c.2247delG frameshift_variant 0.22
embB 4246773 p.Val87Ala missense_variant 0.12
embB 4246945 p.Gln144His missense_variant 0.11
embB 4247122 c.609G>C synonymous_variant 0.14
embB 4247664 p.Tyr384Cys missense_variant 0.11
embB 4247692 c.1179C>T synonymous_variant 0.11
embB 4248726 p.Ser738Phe missense_variant 0.12
embB 4248754 p.Cys747* stop_gained 0.13
embB 4248787 p.Asp758Glu missense_variant 0.15
aftB 4268650 p.Trp63Arg missense_variant 0.29
aftB 4268755 p.Ala28Thr missense_variant 0.14
ubiA 4268930 p.Gly302Ser missense_variant 0.11
ubiA 4269259 p.Arg192His missense_variant 0.12
ubiA 4269293 p.Ala181Thr missense_variant 0.15
ubiA 4269316 p.Ser173Phe missense_variant 0.13
ethA 4326105 p.Leu457Met missense_variant 0.13
ethA 4327124 p.Thr117Ile missense_variant 0.13
ethA 4327148 p.Trp109Leu missense_variant 0.15
whiB6 4338359 p.Ala55Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338694 c.-173A>T upstream_gene_variant 0.15
gid 4407537 c.666G>C synonymous_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0