TB-Profiler result

Run: SRR21673294
Summary

Run ID: SRR21673294

Sample name:

Date: 04-04-2023 02:33:31

Number of reads: 395482

Percentage reads mapped: 99.44

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
tlyA 1918068 c.130delA frameshift_variant 0.14 capreomycin
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 6747 p.Gln503Arg missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7560 p.His87Asn missense_variant 0.13
gyrA 7761 p.Pro154Thr missense_variant 0.12
gyrA 7859 c.558A>G synonymous_variant 0.22
gyrA 7898 c.597C>T synonymous_variant 0.22
gyrA 7963 p.Gly221Glu missense_variant 0.17
gyrA 9338 p.Gln679His missense_variant 0.15
gyrA 9533 c.2232C>G synonymous_variant 0.12
fgd1 490877 p.Met32Thr missense_variant 0.15
mshA 575168 c.-180C>A upstream_gene_variant 0.29
mshA 575184 c.-164G>C upstream_gene_variant 0.29
mshA 575857 c.510G>A synonymous_variant 0.14
mshA 576397 p.Ser350Arg missense_variant 0.13
ccsA 620065 p.Ala59Ser missense_variant 0.13
ccsA 620374 p.Pro162Thr missense_variant 0.11
rpoB 760957 p.Arg384Leu missense_variant 0.13
rpoB 761685 p.Arg627Cys missense_variant 0.11
rpoB 762002 c.2196C>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776582 p.Gln633His missense_variant 0.12
mmpL5 777605 c.876C>G synonymous_variant 0.12
mmpL5 778036 p.Val149Ile missense_variant 0.13
mmpS5 778887 p.Arg7Ser missense_variant 0.13
mmpR5 779123 p.Val45Glu missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781496 c.-64G>A upstream_gene_variant 0.12
rpsL 781641 p.Pro28Thr missense_variant 0.11
rpsL 781845 p.Lys96Glu missense_variant 0.1
rpsL 781912 p.Gly118Asp missense_variant 0.11
rplC 801066 c.258G>A synonymous_variant 0.13
rplC 801085 p.Thr93Ser missense_variant 0.13
fbiC 1303200 c.270G>T synonymous_variant 0.17
fbiC 1304128 p.Gln400* stop_gained 0.12
fbiC 1304517 c.1587C>G synonymous_variant 0.17
Rv1258c 1406878 c.462delT frameshift_variant 0.13
Rv1258c 1406909 c.432C>A synonymous_variant 0.2
Rv1258c 1407308 c.33G>A synonymous_variant 0.17
Rv1258c 1407506 c.-167dupG upstream_gene_variant 0.2
embR 1416982 c.366C>A synonymous_variant 0.14
embR 1417460 c.-113G>A upstream_gene_variant 0.14
atpE 1460915 c.-130C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1673237 c.-203C>A upstream_gene_variant 0.17
fabG1 1673871 p.Ser144Arg missense_variant 0.11
rpsA 1833483 c.-59G>T upstream_gene_variant 0.12
tlyA 1917869 c.-71A>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918372 p.Gly145Cys missense_variant 0.22
tlyA 1918441 p.Val168Phe missense_variant 0.12
ndh 2101757 p.Leu429Arg missense_variant 0.13
ndh 2101876 c.1167C>A synonymous_variant 0.11
katG 2153916 p.Met732Ile missense_variant 0.11
katG 2154790 p.Pro441Gln missense_variant 0.17
katG 2155302 c.810C>T synonymous_variant 0.29
katG 2156123 c.-12G>C upstream_gene_variant 0.11
PPE35 2168139 p.Ala825Asp missense_variant 0.2
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169580 p.Gly345Ser missense_variant 0.14
PPE35 2170365 p.Ala83Val missense_variant 0.33
Rv1979c 2222143 p.Ser341* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288742 p.Thr167Ile missense_variant 0.14
pncA 2289734 c.-493C>A upstream_gene_variant 0.15
kasA 2518129 c.15C>T synonymous_variant 0.22
kasA 2518433 c.319C>A synonymous_variant 0.15
kasA 2518635 p.Gly174Val missense_variant 0.2
kasA 2518819 p.Asp235Glu missense_variant 0.22
eis 2714543 c.790C>A synonymous_variant 0.22
eis 2715161 p.Val58Leu missense_variant 0.12
ahpC 2726735 c.543C>G synonymous_variant 0.12
folC 2746647 p.Gln318Lys missense_variant 0.25
folC 2746976 p.Asp208Val missense_variant 0.15
folC 2746982 p.Gly206Val missense_variant 0.13
folC 2747483 p.Pro39Leu missense_variant 0.17
pepQ 2859569 p.Ala284Ser missense_variant 0.17
pepQ 2859617 p.Ala268Thr missense_variant 0.17
pepQ 2859768 p.Phe217Leu missense_variant 0.13
pepQ 2860143 c.276G>T synonymous_variant 0.15
pepQ 2860199 p.Ala74Ser missense_variant 0.12
ribD 2986818 c.-21C>A upstream_gene_variant 0.14
ribD 2987284 p.Ala149Asp missense_variant 0.11
Rv2752c 3064967 p.Leu409Met missense_variant 0.11
Rv2752c 3065535 c.657C>G synonymous_variant 0.14
Rv2752c 3065938 p.Asp85Val missense_variant 0.13
Rv2752c 3066082 p.Leu37Pro missense_variant 0.11
Rv2752c 3066176 p.Pro6Ser missense_variant 0.14
Rv2752c 3066355 c.-164T>C upstream_gene_variant 0.15
thyX 3067480 p.Asp156Asn missense_variant 0.15
thyX 3067624 p.Tyr108His missense_variant 0.12
thyX 3067820 c.126C>A synonymous_variant 0.14
thyX 3068124 c.-179G>A upstream_gene_variant 0.13
thyA 3074295 c.177G>T synonymous_variant 0.2
thyA 3074445 c.27C>A synonymous_variant 0.12
ald 3087087 p.Ile90Phe missense_variant 0.13
fbiD 3339355 c.238C>T synonymous_variant 0.2
fbiD 3339395 p.Asn93Ser missense_variant 0.18
fbiD 3339491 p.Leu125Pro missense_variant 0.13
fbiD 3339587 p.Ala157Glu missense_variant 0.13
fprA 3473825 c.-182T>C upstream_gene_variant 0.1
fprA 3473837 c.-169delG upstream_gene_variant 0.13
fprA 3474174 c.168T>C synonymous_variant 0.13
fprA 3475375 c.1369T>C stop_lost&splice_region_variant 0.17
whiB7 3568488 c.191delG frameshift_variant 0.12
whiB7 3568534 p.Arg49Met missense_variant 0.1
Rv3236c 3613065 c.50_51delTG frameshift_variant 0.11
fbiA 3640616 c.77delG frameshift_variant 0.12
fbiA 3641163 p.Asp207Glu missense_variant 0.11
fbiB 3641738 p.Glu68Asp missense_variant 0.11
fbiB 3641953 p.Leu140Arg missense_variant 0.13
rpoA 3877688 p.Glu274* stop_gained 0.12
rpoA 3877913 p.Lys199* stop_gained 0.13
clpC1 4038650 c.2055C>A synonymous_variant 0.12
clpC1 4038747 p.Arg653Leu missense_variant 0.18
clpC1 4039340 p.Lys455Asn missense_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4241357 p.Ala499Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244162 c.930G>A synonymous_variant 0.25
embA 4244551 p.Ala440Asp missense_variant 0.13
embA 4244685 p.Ile485Phe missense_variant 0.17
embB 4246665 p.Gln51Leu missense_variant 0.11
embB 4247055 p.Leu181Arg missense_variant 0.12
embB 4247093 p.Gly194Trp missense_variant 0.17
embB 4247525 p.Ala338Ser missense_variant 0.13
embB 4248075 p.Glu521Val missense_variant 0.11
embB 4249401 p.Val963Ala missense_variant 0.2
embB 4249519 c.3006C>T synonymous_variant 0.17
aftB 4267061 p.Leu592Phe missense_variant 0.14
aftB 4267294 p.Ala515Ser missense_variant 0.14
aftB 4267698 p.Leu380Pro missense_variant 0.11
ubiA 4269238 p.Ala199Asp missense_variant 0.15
ethA 4326068 p.Arg469Leu missense_variant 0.11
ethA 4326830 p.Gln215Arg missense_variant 0.13
ethA 4328269 c.-796C>T upstream_gene_variant 0.12
ethA 4328331 c.-858C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408365 c.-163C>A upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0