TB-Profiler result

Run: ERR4800009
Summary

Run ID: ERR4800009

Sample name:

Date: 01-04-2023 09:31:50

Number of reads: 423775

Percentage reads mapped: 98.32

Strain: lineage1.1

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
lineage1 Indo-Oceanic EAI RD239 0.95
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
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 4407851 c.351delG 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
gyrB 6112 p.Met291Ile missense_variant 0.83
gyrB 6124 c.885C>T synonymous_variant 0.82
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7565 c.264C>A synonymous_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.85
gyrA 8684 p.Glu461Asp missense_variant 0.33
gyrA 8721 p.Arg474Trp missense_variant 0.4
gyrA 9083 c.1782G>A synonymous_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 0.82
gyrA 9240 p.Gly647* stop_gained 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491734 p.Arg318Ser missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619804 c.-87G>A upstream_gene_variant 0.12
rpoB 760293 p.Asn163Asp missense_variant 0.15
rpoB 760302 p.Glu166* stop_gained 0.17
rpoB 760339 p.Gly178Val missense_variant 0.12
rpoB 760878 p.Pro358Thr missense_variant 0.5
rpoB 761255 c.1449T>C synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763420 c.51G>A synonymous_variant 0.18
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777245 c.1236G>T synonymous_variant 0.18
mmpL5 777270 p.Gly404Val missense_variant 0.14
mmpL5 778440 p.Pro14Gln missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302776 c.-155C>A upstream_gene_variant 0.17
fbiC 1303097 p.Ala56Val missense_variant 0.12
fbiC 1303154 p.Arg75Leu missense_variant 0.13
fbiC 1303382 p.Pro151Gln missense_variant 0.18
fbiC 1303986 c.1056C>T synonymous_variant 0.12
fbiC 1305156 p.Leu742Phe missense_variant 0.13
embR 1416966 p.Ala128Thr missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 0.93
embR 1417296 p.Pro18Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473154 n.1309C>A non_coding_transcript_exon_variant 0.25
rrl 1474381 n.724T>C non_coding_transcript_exon_variant 1.0
rrl 1475359 n.1702G>T non_coding_transcript_exon_variant 0.67
rrl 1475374 n.1717G>T non_coding_transcript_exon_variant 0.67
rpsA 1833449 c.-93G>T upstream_gene_variant 0.2
rpsA 1833684 p.Arg48Leu missense_variant 0.33
rpsA 1833904 p.Glu121Asp missense_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102181 p.Asp288Asn missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168852 c.1761G>T synonymous_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.14
PPE35 2169506 c.1107G>T synonymous_variant 0.15
PPE35 2169967 p.Asn216Asp missense_variant 1.0
PPE35 2170051 p.Ala188Thr missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 0.85
Rv1979c 2222641 p.Ser175Leu missense_variant 1.0
Rv1979c 2222868 c.297C>A synonymous_variant 0.17
Rv1979c 2223132 c.33C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289369 c.-128C>A upstream_gene_variant 0.27
kasA 2518132 c.18C>T synonymous_variant 0.86
kasA 2518509 p.Gly132Ala missense_variant 0.29
kasA 2518781 p.Pro223Ala missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.93
folC 2746488 p.Asp371Tyr missense_variant 1.0
ribD 2987483 c.645C>A synonymous_variant 0.2
ribD 2987508 p.Ala224Ser missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 0.67
Rv2752c 3064944 c.1248G>A synonymous_variant 0.22
thyA 3073681 c.791G>T stop_lost&splice_region_variant 0.29
thyA 3074406 c.66C>A synonymous_variant 0.17
thyA 3074518 c.-47G>T upstream_gene_variant 0.2
thyA 3074592 c.-121G>T upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339471 c.354G>T synonymous_variant 0.13
Rv3083 3448350 c.-154G>T upstream_gene_variant 0.15
Rv3083 3448405 c.-99G>T upstream_gene_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841578 c.-158G>A upstream_gene_variant 0.22
alr 3841584 c.-164C>A upstream_gene_variant 0.2
rpoA 3877530 c.978C>A synonymous_variant 0.17
rpoA 3877771 p.Ser246* stop_gained 0.12
rpoA 3878622 c.-115C>A upstream_gene_variant 0.18
ddn 3986927 p.Met28Ile missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 0.93
clpC1 4040530 p.Val59Met missense_variant 0.12
embC 4240018 c.156C>A synonymous_variant 0.12
embC 4240476 p.Ala205Val missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241018 c.1156C>T synonymous_variant 0.92
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243202 c.-31C>G upstream_gene_variant 0.29
embA 4243848 p.Val206Met missense_variant 0.94
embA 4244148 p.Trp306Arg missense_variant 0.92
embB 4245524 c.-990G>T upstream_gene_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 0.75
embB 4247345 p.Leu278Met missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 0.95
embB 4248862 c.2349C>A synonymous_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326623 p.Pro284Gln missense_variant 0.2
ethA 4327122 p.Val118Ile missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0