TB-Profiler result

Run: ERR751338

Summary

Run ID: ERR751338

Sample name:

Date: 02-04-2023 04:25:15

Number of reads: 1683032

Percentage reads mapped: 29.78

Strain: lineage5.1.1

Drug-resistance: Other


Download CSV Download TXT Download PDF Download JSON
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 0.98 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 762920 c.-450C>G upstream_gene_variant 0.16
rpoC 762923 c.-447C>G upstream_gene_variant 0.16
rpoB 762925 p.Thr1040Ile missense_variant 0.16
rpoC 762932 c.-438G>A upstream_gene_variant 0.16
rpoB 762939 p.Met1045Leu missense_variant 0.18
rpoB 762942 p.Ile1046Val missense_variant 0.18
rpoC 762947 c.-423C>G upstream_gene_variant 0.19
rpoC 762962 c.-408C>T upstream_gene_variant 0.23
rpoC 762983 c.-387C>T upstream_gene_variant 0.26
rpoC 762989 c.-381G>C upstream_gene_variant 0.26
rpoC 762995 c.-375G>C upstream_gene_variant 0.26
rpoB 763005 p.Cys1067Val missense_variant 0.18
rpoC 763013 c.-357C>A upstream_gene_variant 0.16
rpoB 763014 p.Met1070Leu missense_variant 0.18
rpoC 763028 c.-342T>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.15
rpoC 763041 c.-329C>T upstream_gene_variant 0.13
rpoC 763280 c.-90C>T upstream_gene_variant 1.0
rpoC 764335 c.966G>C synonymous_variant 0.11
rpoC 764348 p.Met327Leu missense_variant 0.12
rpoC 764355 p.Gln329Pro missense_variant 0.12
rpoC 764359 c.990C>G synonymous_variant 0.12
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764582 p.Leu405Met missense_variant 0.16
rpoC 764605 c.1236G>C synonymous_variant 0.18
rpoC 764611 c.1242G>C synonymous_variant 0.17
rpoC 764617 c.1248C>T synonymous_variant 0.18
rpoC 764620 c.1251G>T synonymous_variant 0.17
rpoC 764632 c.1263T>C synonymous_variant 0.22
rpoC 764641 c.1272C>T synonymous_variant 0.22
rpoC 764647 c.1278C>T synonymous_variant 0.22
rpoC 764650 c.1281G>T synonymous_variant 0.22
rpoC 764663 p.Val432Ile missense_variant 0.12
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.49
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.7
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.67
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.7
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.68
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.69
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.64
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.62
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.61
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.55
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.43
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.18
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.18
rrs 1472338 n.493A>T non_coding_transcript_exon_variant 0.17
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.19
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.19
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.2
rrs 1472379 n.534T>A non_coding_transcript_exon_variant 0.2
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.2
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.2
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.18
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.2
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.21
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.19
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.1
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.24
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.61
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.61
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.64
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.73
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.75
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.75
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.68
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.62
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.29
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.3
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.1
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.12
rrl 1474182 n.525C>G non_coding_transcript_exon_variant 0.16
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.16
rrl 1474185 n.528G>C non_coding_transcript_exon_variant 0.16
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.18
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.18
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.18
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.16
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.13
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.13
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.35
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.34
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.34
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.67
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.75
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.74
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.81
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.8
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.78
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.63
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.49
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.34
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.1
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 0.98
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 1.0
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 4038857 c.1848C>A synonymous_variant 0.15
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
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