TB-Profiler result

Run: SRR998627
Summary

Run ID: SRR998627

Sample name:

Date: 04-04-2023 23:28:49

Number of reads: 747985

Percentage reads mapped: 99.08

Strain: lineage6.3.1

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
lineage6.3 West-Africa 2 AFRI_1 RD702 0.43
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.64
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.44
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
embB 4248003 p.Gln497Arg missense_variant 0.17 ethambutol
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 6446 p.Ala403Ser missense_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.43
fgd1 491668 p.Lys296Glu missense_variant 0.65
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576275 p.Asp310His missense_variant 0.12
ccsA 619737 c.-154G>A upstream_gene_variant 0.29
rpoB 760420 p.Trp205Leu missense_variant 0.18
rpoB 760969 p.Ser388Leu missense_variant 0.71
rpoB 761723 p.Glu639Asp missense_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 0.92
rpoC 763280 c.-90C>T upstream_gene_variant 0.48
rpoC 763904 p.Ala179Ser missense_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777986 c.495C>A synonymous_variant 0.18
mmpS5 778820 p.Arg29Pro missense_variant 0.12
mmpR5 779395 p.Leu136Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304304 c.1374C>T synonymous_variant 0.13
fbiC 1305353 p.Gly808Asp missense_variant 0.15
Rv1258c 1406740 p.His201Tyr missense_variant 0.4
Rv1258c 1406830 p.Ile171Val missense_variant 0.12
Rv1258c 1407273 p.Asp23Val missense_variant 0.5
Rv1258c 1407416 c.-76C>T upstream_gene_variant 0.14
atpE 1461130 p.Gly29Val missense_variant 0.13
atpE 1461251 c.207G>T synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475084 n.1427G>T non_coding_transcript_exon_variant 0.14
inhA 1673338 c.-864G>A upstream_gene_variant 0.5
inhA 1674434 p.Val78Ala missense_variant 0.54
tlyA 1917880 c.-60C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918610 p.Gly224Ala missense_variant 0.11
ndh 2101921 c.1122G>A synonymous_variant 0.63
ndh 2102307 p.Gly246Ser missense_variant 0.12
ndh 2102694 p.Val117Ile missense_variant 0.48
ndh 2103112 c.-70G>T upstream_gene_variant 0.64
ndh 2103221 c.-179C>A upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.94
katG 2155503 c.609C>T synonymous_variant 0.43
katG 2156139 c.-28G>T upstream_gene_variant 0.15
katG 2156211 c.-100G>T upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168524 p.Gly697Arg missense_variant 0.13
PPE35 2170307 c.306G>T synonymous_variant 0.18
Rv1979c 2222007 p.Phe386Leu missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 0.88
Rv1979c 2222763 p.Phe134Leu missense_variant 0.18
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289110 c.132C>T synonymous_variant 0.33
pncA 2290062 c.-821G>A upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 0.89
kasA 2519242 c.1129delG frameshift_variant 0.12
eis 2714158 p.Ser392Thr missense_variant 0.12
eis 2715041 p.Arg98Cys missense_variant 0.22
eis 2715384 c.-52C>A upstream_gene_variant 0.17
pepQ 2859509 p.Glu304Lys missense_variant 0.25
ald 3086728 c.-92C>T upstream_gene_variant 0.56
ald 3086788 c.-32T>C upstream_gene_variant 0.73
ald 3086856 p.Glu13Lys missense_variant 0.39
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.29
Rv3083 3449478 c.975C>A synonymous_variant 0.12
Rv3083 3449644 p.Ala381Thr missense_variant 0.6
Rv3083 3449694 c.1191G>C synonymous_variant 0.14
Rv3083 3449781 c.1278G>A synonymous_variant 0.38
Rv3083 3449868 c.1365C>G synonymous_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612749 p.Gly123Ala missense_variant 0.11
alr 3840518 c.903G>C synonymous_variant 0.12
alr 3840932 c.489C>T synonymous_variant 0.75
rpoA 3877641 p.Phe289Leu missense_variant 0.11
rpoA 3877696 p.Thr271Ile missense_variant 0.4
rpoA 3878493 c.15G>A synonymous_variant 0.35
ddn 3986987 c.144G>T synonymous_variant 0.5
ddn 3987180 p.Asp113Asn missense_variant 0.36
clpC1 4040010 p.Ala232Asp missense_variant 0.57
clpC1 4040824 c.-120C>T upstream_gene_variant 0.47
clpC1 4040887 c.-183C>A upstream_gene_variant 0.12
embC 4239843 c.-20A>C upstream_gene_variant 0.71
embC 4240671 p.Thr270Ile missense_variant 0.64
embC 4240814 p.Gly318Ser missense_variant 0.13
embC 4240988 p.Ala376Ser missense_variant 0.18
embC 4241843 p.Leu661Ile missense_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 0.57
embA 4244595 p.Pro455Ser missense_variant 0.15
embA 4244635 p.Val468Ala missense_variant 0.63
embA 4245147 p.Pro639Ser missense_variant 0.38
embA 4246167 p.Met979Val missense_variant 0.12
embB 4246864 c.351C>T synonymous_variant 0.38
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248095 p.Leu528Ile missense_variant 0.15
embB 4249094 p.Ala861Ser missense_variant 0.14
aftB 4267604 c.1233C>T synonymous_variant 0.18
aftB 4268477 c.360C>T synonymous_variant 0.27
aftB 4268924 c.-88C>A upstream_gene_variant 0.12
aftB 4269351 c.-515C>T upstream_gene_variant 0.41
ubiA 4269387 p.Glu149Asp missense_variant 0.89
aftB 4269522 c.-686C>T upstream_gene_variant 0.62
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 0.56
ethR 4326928 c.-621G>A upstream_gene_variant 0.46
ethA 4327103 p.Gly124Asp missense_variant 0.44
ethR 4327942 p.Val132Ile missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.92
gid 4407643 p.Arg187Lys missense_variant 0.2
gid 4408327 c.-125A>G upstream_gene_variant 0.29