TB-Profiler result

Run: ERR502494

Summary

Run ID: ERR502494

Sample name:

Date: 01-04-2023 21:56:09

Number of reads: 3662828

Percentage reads mapped: 68.3

Strain: lineage5.1.1

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 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
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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763280 c.-90C>T upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.13
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.32
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.58
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.61
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.68
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.76
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.73
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.72
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.71
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.71
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.6
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.46
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.46
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.46
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.28
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.44
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.44
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.62
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.59
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.64
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.66
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.71
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.7
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.7
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.74
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.72
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.63
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.39
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.38
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.38
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.36
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.3
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrl 1473871 n.214T>G non_coding_transcript_exon_variant 0.12
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.12
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.12
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.13
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.13
rrl 1473905 n.248T>C non_coding_transcript_exon_variant 0.12
rrl 1474003 n.346G>A non_coding_transcript_exon_variant 0.22
rrl 1474527 n.870T>G non_coding_transcript_exon_variant 0.27
rrl 1474530 n.873G>T non_coding_transcript_exon_variant 0.23
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.23
rrl 1474539 n.882C>A non_coding_transcript_exon_variant 0.21
rrl 1474542 n.885A>C non_coding_transcript_exon_variant 0.21
rrl 1474552 n.895C>G non_coding_transcript_exon_variant 0.2
rrl 1474555 n.898T>G non_coding_transcript_exon_variant 0.21
rrl 1474562 n.905G>C non_coding_transcript_exon_variant 0.2
rrl 1474565 n.908T>A non_coding_transcript_exon_variant 0.2
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.21
rrl 1474571 n.914G>T non_coding_transcript_exon_variant 0.21
rrl 1474578 n.921A>G non_coding_transcript_exon_variant 0.27
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.27
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.27
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.27
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.3
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.3
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.42
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.56
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.72
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.79
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.81
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.85
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.84
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.85
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.93
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.9
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.82
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.77
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.76
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.73
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.71
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.57
rrl 1474931 n.1274G>A non_coding_transcript_exon_variant 0.57
rrl 1474938 n.1281G>A non_coding_transcript_exon_variant 0.58
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.2
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.2
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.2
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.2
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.14
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.15
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.14
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.4
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.52
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.62
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.64
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.78
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.57
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101840 c.1203G>A synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2747784 c.-186C>T upstream_gene_variant 0.99
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878493 c.15G>A synonymous_variant 1.0
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4040462 c.243C>T synonymous_variant 1.0
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269693 c.-857C>T upstream_gene_variant 1.0
ethA 4326567 p.Arg303Trp missense_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338547 c.-26A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0