TB-Profiler result

Run: ERR2229529
Summary

Run ID: ERR2229529

Sample name:

Date: 31-03-2023 17:17:40

Number of reads: 947881

Percentage reads mapped: 99.28

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 5856 p.Ile206Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7432 p.Val44Ala missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.4
ccsA 620501 p.Gly204Val missense_variant 0.14
ccsA 620827 p.Val313Leu missense_variant 0.18
rpoB 759681 c.-126C>A upstream_gene_variant 0.14
rpoB 762858 p.Thr1018Ser missense_variant 0.14
rpoC 764365 c.996C>G synonymous_variant 0.23
rpoC 765806 p.Gln813Lys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777884 c.597C>G synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781573 p.Gln5Arg missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304207 p.Arg426Leu missense_variant 0.2
fbiC 1304382 c.1452G>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.29
rrl 1473844 n.187C>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
rpsA 1834004 p.Met155Leu missense_variant 0.13
rpsA 1834098 p.Ser186Tyr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918622 p.Ser228Ile missense_variant 0.12
ndh 2102575 c.468G>A synonymous_variant 0.17
PPE35 2167918 p.Phe899Ile missense_variant 0.12
PPE35 2168294 c.2319G>A synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.46
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289454 c.-213A>T upstream_gene_variant 0.14
folC 2746928 p.Pro224His missense_variant 0.12
folC 2747065 c.534C>T synonymous_variant 0.12
pepQ 2859628 p.Leu264Ser missense_variant 0.2
pepQ 2860534 c.-116G>T upstream_gene_variant 0.14
Rv2752c 3065897 p.Asp99Asn missense_variant 0.12
thyA 3073783 p.Leu230Arg missense_variant 0.1
thyA 3074114 p.Arg120Cys missense_variant 0.12
fbiD 3339736 p.Thr207Ala missense_variant 0.29
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474026 p.Ala7Asp missense_variant 0.2
fprA 3474096 p.Glu30Asp missense_variant 0.2
fprA 3474268 p.Val88Phe missense_variant 0.12
fprA 3474984 c.978G>T synonymous_variant 0.2
whiB7 3568657 p.Arg8Ile missense_variant 0.18
whiB7 3568705 c.-26A>G upstream_gene_variant 0.14
whiB7 3568870 c.-191G>A upstream_gene_variant 0.14
Rv3236c 3613303 c.-187C>A upstream_gene_variant 0.12
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
panD 4043943 c.339A>G synonymous_variant 0.18
embC 4239823 c.-40C>A upstream_gene_variant 0.22
embC 4241445 p.Asp528Val missense_variant 0.12
embC 4241686 c.1825delA frameshift_variant 0.18
embC 4241777 p.Gly639Cys missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243552 p.Val107Ala missense_variant 0.12
embA 4244062 p.Leu277His missense_variant 0.11
embA 4244907 p.Gly559Ser missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.75
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246567 c.54_55insT frameshift_variant 0.6
embB 4246600 c.87G>A synonymous_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.25
aftB 4267094 c.1743G>T synonymous_variant 0.12
aftB 4267099 p.Ala580Thr missense_variant 0.12
aftB 4268113 p.Ala242Pro missense_variant 0.12
aftB 4268680 p.Glu53* stop_gained 0.12
aftB 4268917 c.-81C>T upstream_gene_variant 0.13
ubiA 4269904 c.-71G>T upstream_gene_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407541 p.Gly221Val missense_variant 0.11
gid 4407970 p.Pro78Leu missense_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0