TB-Profiler result

Run: ERR751330
Summary

Run ID: ERR751330

Sample name:

Date: 02-04-2023 04:24:50

Number of reads: 1469241

Percentage reads mapped: 36.37

Strain: lineage5.1.1

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
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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288885 p.Trp119Cys missense_variant 1.0 pyrazinamide
ethA 4326419 c.1054delG frameshift_variant 1.0 ethionamide, ethionamide
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 762899 c.-471G>C upstream_gene_variant 0.23
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 0.28
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoC 762932 c.-438G>A upstream_gene_variant 0.18
rpoB 762939 p.Met1045Leu missense_variant 0.38
rpoB 762942 p.Ile1046Val missense_variant 0.38
rpoC 762947 c.-423C>G upstream_gene_variant 0.21
rpoC 762953 c.-417G>A upstream_gene_variant 0.15
rpoC 762962 c.-408C>T upstream_gene_variant 0.19
rpoC 762965 c.-405T>C upstream_gene_variant 0.18
rpoC 762980 c.-390T>C upstream_gene_variant 0.12
rpoC 762983 c.-387C>T upstream_gene_variant 0.36
rpoC 762989 c.-381G>C upstream_gene_variant 0.31
rpoC 762995 c.-375G>C upstream_gene_variant 0.19
rpoB 763005 p.Cys1067Gly missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763280 c.-90C>T upstream_gene_variant 1.0
rpoC 764557 p.Asn396Lys missense_variant 0.12
rpoC 764575 c.1206T>G synonymous_variant 0.28
rpoC 764581 c.1212T>C synonymous_variant 0.24
rpoC 764582 p.Leu405Met missense_variant 0.24
rpoC 764605 c.1236G>C synonymous_variant 0.21
rpoC 764611 c.1242G>C synonymous_variant 0.22
rpoC 764617 c.1248C>T synonymous_variant 0.21
rpoC 764620 c.1251G>T synonymous_variant 0.22
rpoC 764632 c.1263T>C synonymous_variant 0.21
rpoC 764641 c.1272C>T synonymous_variant 0.22
rpoC 764647 c.1278C>T synonymous_variant 0.2
rpoC 764650 c.1281G>T synonymous_variant 0.22
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 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.14
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.15
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.15
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.59
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.65
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.51
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.65
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.6
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.68
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.67
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.64
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.6
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.51
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.36
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.18
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.23
rrs 1472338 n.493A>T non_coding_transcript_exon_variant 0.26
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.24
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.28
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.31
rrs 1472379 n.534T>A non_coding_transcript_exon_variant 0.29
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.34
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.26
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.29
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.25
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.23
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.2
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.25
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.41
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.22
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.47
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.64
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.66
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.63
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.6
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.28
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.27
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.12
rrl 1474182 n.525C>G non_coding_transcript_exon_variant 0.14
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.13
rrl 1474185 n.528G>C non_coding_transcript_exon_variant 0.13
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.13
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.13
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.15
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.15
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.15
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.15
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.15
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.15
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.15
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.18
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.46
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.45
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.42
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.42
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.43
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.43
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.17
rrl 1475894 n.2237C>G non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.52
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.64
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.57
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.58
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.59
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.59
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.76
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.84
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.76
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.7
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.68
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.41
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.21
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G 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
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 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
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0