TB-Profiler result

Run: ERR2229563

Summary

Run ID: ERR2229563

Sample name:

Date: 31-03-2023 17:18:59

Number of reads: 490790

Percentage reads mapped: 99.26

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7640 p.Gln113His missense_variant 0.22
fgd1 491589 p.Glu269Asp missense_variant 0.17
mshA 576601 c.1254C>T synonymous_variant 0.25
rpoB 760232 c.426G>A synonymous_variant 0.13
rpoB 762588 p.Thr928Ala missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775881 p.Asn867Ile missense_variant 0.29
mmpL5 777157 c.1324C>A synonymous_variant 0.29
mmpL5 777164 c.1317C>T synonymous_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.5
fbiC 1303155 c.225G>A synonymous_variant 0.33
fbiC 1303494 p.Leu188Phe missense_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406192 c.1149G>A synonymous_variant 0.12
atpE 1460916 c.-129G>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474974 n.1317G>A non_coding_transcript_exon_variant 0.14
rrl 1475227 n.1570T>C non_coding_transcript_exon_variant 0.11
rrl 1475962 n.2305G>T non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
inhA 1674457 p.Asn86Tyr missense_variant 0.17
rpsA 1834553 p.Val338Phe missense_variant 0.11
rpsA 1834797 p.Ala419Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155290 p.Lys274Asn missense_variant 0.2
katG 2155763 p.Asp117Tyr missense_variant 0.2
PPE35 2167759 p.Gly952Cys missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.29
PPE35 2167868 c.2745A>C synonymous_variant 0.33
PPE35 2168150 c.2463T>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2169674 c.939T>C synonymous_variant 0.12
PPE35 2169986 p.Leu209Ile missense_variant 0.17
PPE35 2170025 c.588G>A synonymous_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.42
PPE35 2170403 c.210C>G synonymous_variant 0.11
PPE35 2170528 p.Ser29Ala missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223352 c.-188G>A upstream_gene_variant 0.2
kasA 2518809 p.Lys232Arg missense_variant 0.4
eis 2715367 c.-35G>T upstream_gene_variant 0.12
ahpC 2726705 p.Asp171Glu missense_variant 0.2
ribD 2986789 c.-50A>T upstream_gene_variant 0.18
fbiD 3339149 p.Gly11Val missense_variant 0.25
fbiD 3339736 p.Thr207Ala missense_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3473948 c.-59C>T upstream_gene_variant 0.12
fprA 3473965 c.-42A>G upstream_gene_variant 0.12
fprA 3474632 p.Thr209Lys missense_variant 0.17
fprA 3474653 p.Ala216Val missense_variant 0.18
fbiB 3641409 c.-126G>T upstream_gene_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3878158 c.329_349delTCGTGCCGCCGGCCGGCGTCA disruptive_inframe_deletion 0.25
rpoA 3878182 p.Asp109Gly missense_variant 0.22
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.14
panD 4044301 c.-20G>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242875 p.Glu1005Lys missense_variant 0.14
embA 4243408 p.Thr59Ser missense_variant 0.25
embA 4245214 p.Ala661Val missense_variant 0.15
embA 4246106 c.2878delC frameshift_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4247580 p.Ala356Asp missense_variant 0.2
embB 4248490 c.1977G>T synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0