TB-Profiler result

Run: ERR2229546
Summary

Run ID: ERR2229546

Sample name:

Date: 31-03-2023 17:18:16

Number of reads: 712592

Percentage reads mapped: 99.37

Strain: lineage4.8

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
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
pncA 2289057 p.Pro62Gln missense_variant 0.15 pyrazinamide
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 6152 p.Ala305Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9351 p.Ser684Pro missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576566 c.1219C>A synonymous_variant 0.4
ccsA 620383 p.Pro165Ser missense_variant 0.4
ccsA 620497 p.Leu203Met missense_variant 0.29
rpoB 759665 c.-142C>A upstream_gene_variant 0.12
rpoB 760777 p.Ser324* stop_gained 0.22
rpoC 764540 p.Val391Phe missense_variant 0.29
rpoC 765803 p.Thr812Ala missense_variant 0.33
rpoC 767050 p.Gln1227His missense_variant 0.4
rpoC 767185 c.3816G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776015 p.Ile822Val missense_variant 0.2
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.25
mmpL5 777634 p.Gly283Cys missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781674 p.Thr39Ser missense_variant 0.14
rpsL 781748 c.189C>T synonymous_variant 0.18
rplC 801100 p.Gly98Trp missense_variant 0.2
fbiC 1303215 c.285C>A synonymous_variant 0.12
fbiC 1303627 p.Ser233Gly missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303790 c.862delC frameshift_variant 0.18
fbiC 1303992 p.Trp354Cys missense_variant 0.15
fbiC 1304799 c.1869G>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472411 n.566G>A non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474875 n.1218G>T non_coding_transcript_exon_variant 0.13
rrl 1475412 n.1755G>T non_coding_transcript_exon_variant 0.22
rrl 1475810 n.2153T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
inhA 1674233 p.Leu11Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918435 p.Ala166Thr missense_variant 0.18
ndh 2102411 p.Val211Gly missense_variant 0.25
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.21
PPE35 2167868 c.2745A>C synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169178 p.Ala479Ser missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.32
Rv1979c 2222291 p.Ala292Ser missense_variant 0.18
Rv1979c 2222300 p.Val289Leu missense_variant 0.18
Rv1979c 2222311 p.Ser285* stop_gained 0.15
Rv1979c 2222315 p.Ala284Ser missense_variant 0.15
Rv1979c 2222358 c.807C>A synonymous_variant 0.12
Rv1979c 2222674 p.Gly164Val missense_variant 0.18
Rv1979c 2222913 c.252C>T synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288685 p.Ser186Tyr missense_variant 0.15
pncA 2289529 c.-288G>T upstream_gene_variant 0.22
pncA 2290143 c.-903delA upstream_gene_variant 0.29
eis 2714264 p.Gly357Cys missense_variant 0.14
folC 2746144 c.1454delA frameshift_variant 0.22
folC 2747418 p.Gln61Lys missense_variant 0.2
folC 2747569 p.Asp10Glu missense_variant 0.12
pepQ 2859462 c.957C>A synonymous_variant 0.14
pepQ 2859623 p.Pro266Ser missense_variant 0.4
Rv2752c 3064685 p.Ala503Ser missense_variant 0.17
Rv2752c 3065897 p.Asp99Asn missense_variant 0.25
Rv2752c 3066252 c.-61C>A upstream_gene_variant 0.17
Rv2752c 3067157 c.-966G>T upstream_gene_variant 0.12
thyX 3067552 p.Leu132Met missense_variant 0.2
thyA 3073992 p.Ser160Arg missense_variant 0.14
ald 3087188 c.369C>T synonymous_variant 0.18
fprA 3474208 c.206delA frameshift_variant 0.15
fprA 3474225 p.Asp73Glu missense_variant 0.14
fprA 3474917 p.Ala304Val missense_variant 0.2
fprA 3474979 p.Arg325Ser missense_variant 0.22
whiB7 3568424 p.Pro86Thr missense_variant 0.25
Rv3236c 3613172 c.-56C>A upstream_gene_variant 0.17
alr 3840623 c.798C>A synonymous_variant 0.14
rpoA 3877804 p.Gly235Val missense_variant 0.12
rpoA 3878350 p.Ser53Ile missense_variant 0.18
clpC1 4038589 p.Arg706Ser missense_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.29
embC 4240292 p.Leu144Met missense_variant 0.17
embC 4240310 p.Pro150Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242874 p.Asp1004Glu missense_variant 0.2
embA 4243476 p.Leu82Met missense_variant 0.12
embA 4244449 p.Ala406Asp missense_variant 0.13
embA 4244452 p.Pro407Gln missense_variant 0.13
embA 4244476 p.Ala415Glu missense_variant 0.17
embA 4244718 p.Tyr496His missense_variant 0.22
embA 4244966 c.1734C>T synonymous_variant 0.18
embA 4245258 p.Val676Phe missense_variant 0.15
embA 4245407 c.2175G>T synonymous_variant 0.17
embB 4247536 c.1023C>A synonymous_variant 0.33
embB 4249613 p.Gly1034Ser missense_variant 0.2
aftB 4267102 p.Arg579Ser missense_variant 0.17
aftB 4268456 c.381G>T synonymous_variant 0.29
ethA 4326885 p.Ser197Pro missense_variant 0.14
ethA 4327677 c.-204G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407682 p.His174Leu missense_variant 0.18
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0