TB-Profiler result

Run: SRR998625
Summary

Run ID: SRR998625

Sample name:

Date: 04-04-2023 23:28:43

Number of reads: 738490

Percentage reads mapped: 99.08

Strain: lineage6.3.1

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
lineage6 West-Africa 2 AFRI_1 RD702 0.4
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.59
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.36
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 5070 c.-170C>G upstream_gene_variant 0.13
gyrB 6446 p.Ala403Ser missense_variant 0.95
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8885 c.1584C>A synonymous_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.62
fgd1 491668 p.Lys296Glu missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 0.94
ccsA 620673 p.Trp261Cys missense_variant 0.14
rpoB 760969 p.Ser388Leu missense_variant 0.5
rpoB 761723 p.Glu639Asp missense_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763280 c.-90C>T upstream_gene_variant 0.33
rpoC 763904 p.Ala179Ser missense_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>A synonymous_variant 0.14
mmpL5 776045 c.2436G>A synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 0.8
mmpL5 778684 c.-204C>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406740 p.His201Tyr missense_variant 0.47
Rv1258c 1407132 p.Gly70Val missense_variant 0.12
Rv1258c 1407205 p.Ile46Val missense_variant 0.15
Rv1258c 1407273 p.Asp23Val missense_variant 0.5
embR 1416401 p.Asn316Ser missense_variant 0.14
embR 1416989 c.358delA frameshift_variant 0.18
atpE 1461016 c.-29C>A upstream_gene_variant 0.15
atpE 1461050 p.Asp2Glu missense_variant 0.12
atpE 1461251 c.207G>T synonymous_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.12
inhA 1673338 c.-864G>A upstream_gene_variant 0.6
inhA 1674434 p.Val78Ala missense_variant 0.29
rpsA 1834171 c.630C>G synonymous_variant 0.12
rpsA 1834963 c.1422G>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.62
ndh 2102694 p.Val117Ile missense_variant 0.56
ndh 2102967 p.Gly26Trp missense_variant 0.12
ndh 2103112 c.-70G>T upstream_gene_variant 0.58
katG 2154465 p.Cys549* stop_gained 0.12
katG 2154724 p.Arg463Leu missense_variant 0.93
katG 2155503 c.609C>T synonymous_variant 0.5
katG 2155995 p.Trp39Cys missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168625 p.Thr663Asn missense_variant 0.11
PPE35 2169307 p.Asp436Asn missense_variant 0.12
PPE35 2169715 p.Gly300Ser missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222757 c.408G>T synonymous_variant 0.33
Rv1979c 2222852 p.Ala105Thr missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289888 c.-647G>T upstream_gene_variant 0.25
pncA 2290062 c.-821G>A upstream_gene_variant 0.69
kasA 2518132 c.18C>T synonymous_variant 0.85
kasA 2518750 p.Met212Ile missense_variant 0.13
pepQ 2860083 c.336C>T synonymous_variant 0.12
Rv2752c 3065593 p.Leu200Pro missense_variant 0.15
thyA 3074664 c.-193G>T upstream_gene_variant 0.11
ald 3086728 c.-92C>T upstream_gene_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 0.43
ald 3086856 p.Glu13Lys missense_variant 0.38
ald 3087084 c.266delA frameshift_variant 0.94
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.53
Rv3083 3448437 c.-67C>G upstream_gene_variant 0.12
Rv3083 3449644 p.Ala381Thr missense_variant 0.5
Rv3083 3449781 c.1278G>A synonymous_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475343 p.Ser446Ile missense_variant 0.11
fprA 3475366 p.Gly454Arg missense_variant 0.12
Rv3236c 3612871 p.Phe82Leu missense_variant 0.13
fbiB 3641022 c.-513C>A upstream_gene_variant 0.12
fbiB 3641328 c.-207T>C upstream_gene_variant 0.13
fbiB 3641594 c.60G>C synonymous_variant 0.12
alr 3840932 c.489C>T synonymous_variant 0.53
alr 3841006 p.Asp139Tyr missense_variant 0.12
rpoA 3877696 p.Thr271Ile missense_variant 0.25
rpoA 3878493 c.15G>A synonymous_variant 0.75
ddn 3986987 c.144G>T synonymous_variant 0.58
ddn 3987180 p.Asp113Asn missense_variant 0.83
clpC1 4040010 p.Ala232Asp missense_variant 0.64
clpC1 4040824 c.-120C>T upstream_gene_variant 0.85
panD 4044306 c.-25T>C upstream_gene_variant 0.22
embC 4239843 c.-20A>C upstream_gene_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243493 c.261C>G synonymous_variant 0.12
embA 4244024 p.Trp264Cys missense_variant 0.12
embA 4244220 c.988C>T synonymous_variant 0.9
embA 4244379 p.Pro383Ser missense_variant 0.38
embA 4245147 p.Pro639Ser missense_variant 0.45
embA 4245657 p.Ser809Pro missense_variant 0.18
embB 4245908 c.-606G>T upstream_gene_variant 0.15
embB 4246864 c.351C>T synonymous_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267411 p.Gly476Arg missense_variant 0.11
aftB 4268072 p.Ile255Met missense_variant 0.11
aftB 4268477 c.360C>T synonymous_variant 0.65
aftB 4269351 c.-515C>T upstream_gene_variant 0.38
ubiA 4269387 p.Glu149Asp missense_variant 0.93
aftB 4269522 c.-686C>T upstream_gene_variant 0.36
aftB 4269606 c.-770T>C upstream_gene_variant 0.88
ubiA 4270014 c.-181C>G upstream_gene_variant 0.12
ethA 4326465 p.Ile337Val missense_variant 0.46
ethR 4326928 c.-621G>A upstream_gene_variant 0.5
ethA 4327103 p.Gly124Asp missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407734 p.Gly157Arg missense_variant 0.15
gid 4407847 p.Ala119Asp missense_variant 0.13
gid 4408327 c.-125A>G upstream_gene_variant 0.23