TB-Profiler result

Run: ERR2514125
Summary

Run ID: ERR2514125

Sample name:

Date: 31-03-2023 20:08:04

Number of reads: 814161

Percentage reads mapped: 93.9

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
gid 4408087 c.115delC frameshift_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
gyrA 6760 c.-542G>C upstream_gene_variant 0.1
gyrA 6796 c.-506C>T upstream_gene_variant 0.13
gyrB 6798 p.Gly520Ala missense_variant 0.14
gyrA 6808 c.-494C>G upstream_gene_variant 0.15
gyrA 6811 c.-491C>T upstream_gene_variant 0.13
gyrA 6824 c.-478C>T upstream_gene_variant 0.12
gyrA 6841 c.-461T>C upstream_gene_variant 0.1
gyrA 6869 c.-433T>C upstream_gene_variant 0.11
gyrA 6872 c.-430T>C upstream_gene_variant 0.1
gyrA 7066 c.-236G>C upstream_gene_variant 0.11
gyrA 7072 c.-230G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576207 p.Ala287Asp missense_variant 0.12
rpoB 760817 c.1011A>G synonymous_variant 0.1
rpoB 760820 c.1014T>C synonymous_variant 0.1
rpoB 760826 c.1020C>G synonymous_variant 0.12
rpoB 760830 c.1024T>C synonymous_variant 0.12
rpoB 760841 c.1035T>C synonymous_variant 0.13
rpoB 760858 p.Val351Ala missense_variant 0.12
rpoB 760862 c.1056G>C synonymous_variant 0.12
rpoB 760869 p.Val355Leu missense_variant 0.11
rpoB 760877 c.1071G>C synonymous_variant 0.11
rpoB 760883 c.1077G>C synonymous_variant 0.11
rpoB 760886 c.1080A>G synonymous_variant 0.11
rpoB 760887 p.Thr361Ala missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764405 c.1036A>C synonymous_variant 0.12
rpoC 764431 c.1062G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.14
rpoC 764458 c.1089G>C synonymous_variant 0.2
rpoC 764461 c.1092A>G synonymous_variant 0.2
rpoC 764497 c.1128A>G synonymous_variant 0.11
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 766315 c.2946C>G synonymous_variant 0.11
rpoC 766348 c.2979A>G synonymous_variant 0.15
rpoC 766381 c.3012C>T synonymous_variant 0.17
rpoC 766384 c.3015A>G synonymous_variant 0.17
rpoC 766390 c.3021C>T synonymous_variant 0.16
rpoC 766408 c.3039C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777885 p.Ala199Ile missense_variant 0.12
mmpL5 777888 p.Gln198Leu missense_variant 0.12
mmpL5 777891 p.Gln197Leu missense_variant 0.12
mmpL5 777894 p.Gln196Leu missense_variant 0.12
mmpL5 777896 p.Asp195Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303988 p.Asp353Val missense_variant 0.11
fbiC 1304834 p.Pro635Leu missense_variant 0.14
Rv1258c 1406088 p.Ala418Asp missense_variant 1.0
embR 1416764 p.Glu195Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 1.0
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 1.0
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 1.0
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.4
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.75
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.6
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.14
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.15
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.14
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.18
rrl 1476665 n.3008T>A non_coding_transcript_exon_variant 0.15
rrl 1476666 n.3009C>T non_coding_transcript_exon_variant 0.14
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.15
rrl 1476684 n.3027C>T non_coding_transcript_exon_variant 0.14
rpsA 1833727 c.186G>C synonymous_variant 0.16
rpsA 1833787 c.246C>G synonymous_variant 0.13
rpsA 1834297 c.756C>T synonymous_variant 0.15
rpsA 1834303 c.762T>G synonymous_variant 0.18
rpsA 1834306 c.765T>C synonymous_variant 0.18
rpsA 1834339 c.798C>T synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101877 p.Gly389Asp missense_variant 0.12
ndh 2102389 c.654G>C synonymous_variant 0.12
ndh 2102392 c.651C>A synonymous_variant 0.12
ndh 2102401 c.642T>C synonymous_variant 0.1
ndh 2102407 c.636T>C synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064822 p.Val457Ala missense_variant 0.11
Rv2752c 3064825 p.Asp456Val missense_variant 0.11
Rv2752c 3064828 p.Gly455Asp missense_variant 0.11
thyA 3074648 c.-177T>G upstream_gene_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339667 p.Gly184Cys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642098 c.564G>A synonymous_variant 1.0
alr 3840636 p.Pro262Gln missense_variant 1.0
rpoA 3878070 c.438T>C synonymous_variant 0.11
rpoA 3878079 c.429C>T synonymous_variant 0.13
rpoA 3878082 c.426T>C synonymous_variant 0.12
rpoA 3878118 c.390T>C synonymous_variant 0.12
rpoA 3878127 c.381G>C synonymous_variant 0.12
rpoA 3878130 c.378C>G synonymous_variant 0.11
rpoA 3878143 p.Gly122Asp missense_variant 0.11
rpoA 3878160 c.348C>G synonymous_variant 0.13
rpoA 3878169 c.339G>C synonymous_variant 0.12
rpoA 3878428 p.Glu27Gly missense_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 1.0
clpC1 4038740 c.1965G>C synonymous_variant 0.1
clpC1 4038818 c.1887G>A synonymous_variant 0.12
clpC1 4038842 c.1863G>T synonymous_variant 0.12
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 0.12
clpC1 4038860 c.1845G>T synonymous_variant 0.14
clpC1 4039805 c.900C>T synonymous_variant 0.13
clpC1 4039814 c.891C>G synonymous_variant 0.14
clpC1 4039817 c.888A>C synonymous_variant 0.14
clpC1 4039820 c.885T>G synonymous_variant 0.14
clpC1 4039826 c.879C>G synonymous_variant 0.13
clpC1 4039831 c.874T>C synonymous_variant 0.13
clpC1 4039850 c.855T>C synonymous_variant 0.12
clpC1 4039865 c.840T>C synonymous_variant 0.1
clpC1 4039904 c.801A>G synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244210 c.978G>A synonymous_variant 0.13
embA 4245567 p.Glu779Lys missense_variant 0.14
embA 4245883 p.Gly884Asp missense_variant 1.0
ethA 4326230 p.Asp415Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0