TB-Profiler result

Run: SRR13861326
Summary

Run ID: SRR13861326

Sample name:

Date: 03-04-2023 09:29:16

Number of reads: 2297538

Percentage reads mapped: 57.49

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
embB 4247891 p.Arg460Cys missense_variant 0.93 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
gyrB 6088 c.849C>A synonymous_variant 1.0
rpoB 760181 c.375T>C synonymous_variant 0.14
rpoB 760184 c.378A>G synonymous_variant 0.14
rpoB 760328 c.522G>C synonymous_variant 0.13
rpoB 760730 c.924T>C synonymous_variant 0.14
rpoB 761786 c.1980C>T synonymous_variant 0.92
rpoC 763945 c.576T>C synonymous_variant 0.14
rpoC 763960 c.591T>C synonymous_variant 0.14
rpoC 763967 p.Gly200Ser missense_variant 0.13
rpoC 764040 p.Ser224Asn missense_variant 0.13
rpoC 764626 c.1257C>T synonymous_variant 0.13
rpoC 764973 p.Asp535Ala missense_variant 0.93
rpoC 766390 c.3021C>T synonymous_variant 0.13
rpoC 766408 c.3039C>T synonymous_variant 0.14
rpoC 766426 c.3057C>T synonymous_variant 0.15
rpoC 766447 c.3078T>C synonymous_variant 0.14
rpoC 766483 c.3114G>C synonymous_variant 0.14
rpoC 766484 p.Val1039Ile missense_variant 0.14
rpoC 766492 c.3123T>C synonymous_variant 0.14
rpoC 766495 c.3126C>T synonymous_variant 0.15
rpoC 766522 c.3153C>G synonymous_variant 0.16
rpoC 766528 c.3159T>C synonymous_variant 0.17
rpoC 766531 c.3162G>T synonymous_variant 0.17
rpoC 766543 c.3174C>T synonymous_variant 0.17
rpoC 766549 c.3180G>C synonymous_variant 0.18
rpoC 766573 c.3204T>C synonymous_variant 0.17
rpoC 766583 p.Gly1072Ser missense_variant 0.19
rpoC 766588 c.3219G>A synonymous_variant 0.18
rpoC 766591 c.3222A>G synonymous_variant 0.19
rpoC 766594 c.3225G>C synonymous_variant 0.2
rpoC 766607 p.Ile1080Leu missense_variant 0.17
rpoC 766630 c.3261G>C synonymous_variant 0.17
rpoC 766645 c.3276A>G synonymous_variant 0.16
rpoC 766651 c.3282T>C synonymous_variant 0.18
rpoC 766657 c.3288A>G synonymous_variant 0.16
rpoC 766672 c.3303T>C synonymous_variant 0.15
rpoC 766738 c.3369G>T synonymous_variant 0.12
rpoC 766750 c.3381C>G synonymous_variant 0.14
rpoC 766933 c.3564A>G synonymous_variant 0.14
rpoC 766945 c.3576A>G synonymous_variant 0.15
rpoC 766963 c.3594T>C synonymous_variant 0.14
rpoC 766996 c.3627C>T synonymous_variant 0.14
rpoC 767009 p.Ser1214Thr missense_variant 0.14
rpoC 767014 c.3645G>C synonymous_variant 0.14
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.14
rpoC 767059 c.3690T>G synonymous_variant 0.15
rpoC 767062 c.3693C>A synonymous_variant 0.16
rpoC 767074 c.3705T>C synonymous_variant 0.14
rpoC 767098 c.3729T>C synonymous_variant 0.15
rpoC 767119 c.3750A>G synonymous_variant 0.16
rpoC 767134 c.3765C>G synonymous_variant 0.14
rpoC 767158 c.3789T>C synonymous_variant 0.14
rpoC 767167 c.3798C>G synonymous_variant 0.15
rpoC 767180 p.Ala1271Gln missense_variant 0.15
rpoC 767191 c.3822C>G synonymous_variant 0.16
rpsL 781532 c.-28G>T upstream_gene_variant 1.0
fbiC 1302843 c.-88A>C upstream_gene_variant 1.0
fbiC 1302887 c.-43delG upstream_gene_variant 1.0
rrl 1473434 n.-224T>C upstream_gene_variant 0.97
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 0.91
rpsA 1833724 c.183C>G synonymous_variant 0.16
rpsA 1833727 c.186G>C synonymous_variant 0.16
rpsA 1833742 c.201A>G synonymous_variant 0.14
rpsA 1833787 c.246C>G synonymous_variant 0.14
rpsA 1833790 c.249T>A synonymous_variant 0.13
rpsA 1833799 c.258C>G synonymous_variant 0.14
rpsA 1833856 c.315A>G synonymous_variant 0.13
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834366 c.825A>G synonymous_variant 0.14
rpsA 1834375 c.834G>A synonymous_variant 0.14
rpsA 1834396 c.855G>C synonymous_variant 0.14
rpsA 1834411 c.870T>C synonymous_variant 0.13
rpsA 1834435 c.894G>C synonymous_variant 0.14
rpsA 1834474 c.933C>G synonymous_variant 0.13
rpsA 1834498 c.957C>T synonymous_variant 0.13
katG 2156364 c.-253T>G upstream_gene_variant 1.0
Rv1979c 2221814 p.Leu451Val missense_variant 1.0
Rv1979c 2222030 p.Val379Met missense_variant 1.0
kasA 2518687 c.573C>T synonymous_variant 0.13
kasA 2518696 c.582C>G synonymous_variant 0.13
kasA 2518717 c.603C>T synonymous_variant 0.15
kasA 2518723 p.Glu203Asp missense_variant 0.14
kasA 2518732 c.618C>G synonymous_variant 0.15
kasA 2519238 p.Thr375Lys missense_variant 1.0
folC 2747285 p.Val105Ala missense_variant 0.97
pepQ 2859712 p.Thr236Ser missense_variant 1.0
Rv2752c 3065064 c.1128G>T synonymous_variant 1.0
thyX 3068085 c.-140T>A upstream_gene_variant 0.99
ald 3087003 p.Asp62His missense_variant 1.0
Rv3083 3448914 p.Ile137Met missense_variant 1.0
fprA 3475146 c.1141delA frameshift_variant 1.0
whiB7 3568676 p.Ser2Pro missense_variant 1.0
fbiA 3641491 p.Ala317Pro missense_variant 1.0
alr 3840235 p.Gly396* stop_gained 0.99
alr 3840304 c.1116delT frameshift_variant 0.94
alr 3841263 p.Arg53His missense_variant 1.0
rpoA 3878082 c.426T>C synonymous_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 0.12
embC 4240706 p.Val282Thr missense_variant 0.13
embC 4240726 c.864G>C synonymous_variant 0.15
embC 4240789 c.927T>C synonymous_variant 0.14
embC 4241029 p.Trp389* stop_gained 0.95
embB 4249631 p.Thr1040Pro missense_variant 0.98
ethA 4327197 p.Gly93Arg missense_variant 1.0