TB-Profiler result

Run: ERR4815075
Summary

Run ID: ERR4815075

Sample name:

Date: 01-04-2023 13:39:19

Number of reads: 726016

Percentage reads mapped: 97.47

Strain: lineage3

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.99
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
rpoB 761115 p.Asn437Asp missense_variant 0.11 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.27 streptomycin
katG 2155790 p.His108Asp missense_variant 0.2 isoniazid
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 5547 p.Leu103Arg missense_variant 0.12
gyrB 5565 p.Phe109Ser missense_variant 0.14
gyrB 6139 c.900G>A synonymous_variant 0.12
gyrB 6735 p.Asn499Ser missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8880 p.Lys527* stop_gained 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491721 c.939A>G synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761865 p.Gly687Cys missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762508 p.Leu901Pro missense_variant 0.14
rpoB 762640 p.Gly945Glu missense_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763164 p.Lys1120* stop_gained 0.18
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 766378 c.3009C>T synonymous_variant 0.13
rpoC 766381 c.3012C>T synonymous_variant 0.13
rpoC 766384 c.3015A>G synonymous_variant 0.13
rpoC 766387 c.3018C>G synonymous_variant 0.14
rpoC 766393 c.3024C>G synonymous_variant 0.14
rpoC 766423 c.3054T>C synonymous_variant 0.18
rpoC 766426 c.3057C>T synonymous_variant 0.2
rpoC 766432 c.3063T>C synonymous_variant 0.18
rpoC 766434 p.Glu1022Gly missense_variant 0.17
rpoC 766447 c.3078T>C synonymous_variant 0.14
rpoC 766450 c.3081T>C synonymous_variant 0.14
rpoC 766559 p.Ile1064Phe missense_variant 0.11
rpoC 766981 c.3612T>G synonymous_variant 0.13
rpoC 767002 c.3633G>C synonymous_variant 0.2
rpoC 767008 c.3639G>T synonymous_variant 0.2
rpoC 767012 c.3643C>T synonymous_variant 0.18
rpoC 767017 c.3648C>T synonymous_variant 0.2
rpoC 767023 p.Asp1218Glu missense_variant 0.17
rpoC 767030 c.3661C>T synonymous_variant 0.18
rpoC 767041 c.3672G>T synonymous_variant 0.18
rpoC 767044 c.3675G>C synonymous_variant 0.17
rpoC 767053 c.3684G>A synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776824 p.Met553Leu missense_variant 0.17
mmpL5 777051 p.Gly477Val missense_variant 0.14
mmpL5 778155 p.Tyr109Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800965 p.Ala53Thr missense_variant 0.18
fbiC 1304381 p.Ala484Val missense_variant 0.29
embR 1416222 p.Phe376Leu missense_variant 0.2
embR 1416232 p.Cys372Gly missense_variant 0.18
embR 1416259 c.1089G>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472671 n.826G>A non_coding_transcript_exon_variant 0.33
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.33
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.33
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.33
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.33
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.33
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.33
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.5
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.44
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.29
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.25
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.25
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.29
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.29
rrl 1475312 n.1655C>T non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.29
rpsA 1833811 c.270G>T synonymous_variant 0.15
rpsA 1833829 c.288A>G synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101953 p.Tyr364His missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 0.89
katG 2154741 p.Ser457Arg missense_variant 0.22
katG 2156248 c.-137C>T upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223111 c.54C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288995 p.Pro83Ser missense_variant 0.1
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714238 c.1095C>T synonymous_variant 0.11
eis 2715242 c.90delT frameshift_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746146 p.Asp485Tyr missense_variant 0.14
thyX 3067678 p.Thr90Ser missense_variant 0.12
Rv3083 3449322 c.819A>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474119 c.114delG frameshift_variant 0.17
fprA 3474404 p.Asn133Ser missense_variant 0.2
fbiB 3641723 c.192dupC frameshift_variant 0.13
fbiB 3642010 p.Gly159Asp missense_variant 0.2
fbiB 3642154 p.Gly207Asp missense_variant 0.11
clpC1 4038506 c.2199G>T synonymous_variant 0.15
clpC1 4039610 c.1095G>C synonymous_variant 0.15
clpC1 4040795 c.-91A>G upstream_gene_variant 0.11
clpC1 4040859 c.-155T>C upstream_gene_variant 0.11
panD 4044421 c.-140G>A upstream_gene_variant 0.12
panD 4044429 c.-148C>T upstream_gene_variant 0.14
embC 4239685 c.-178G>A upstream_gene_variant 1.0
embC 4239730 c.-133T>A upstream_gene_variant 0.15
embC 4240435 c.573C>T synonymous_variant 0.13
embC 4240464 c.604_606delACC conservative_inframe_deletion 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242563 p.Ala901Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243348 p.Thr39Ile missense_variant 0.12
embA 4243373 c.141G>A synonymous_variant 0.11
embA 4243825 p.Thr198Met missense_variant 0.11
embB 4247436 p.Arg308Gln missense_variant 0.13
embB 4248140 p.Phe543Leu missense_variant 0.11
embB 4248820 c.2307C>T synonymous_variant 0.15
aftB 4267206 c.1630delG frameshift_variant 0.22
aftB 4267345 p.Val498Phe missense_variant 0.14
ubiA 4269339 c.494delG frameshift_variant 0.13
ethR 4327687 p.Val47Phe missense_variant 0.22
whiB6 4338334 p.Ala63Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0