TB-Profiler result

Run: SRR13837579
Summary

Run ID: SRR13837579

Sample name:

Date: 03-04-2023 09:13:42

Number of reads: 597205

Percentage reads mapped: 96.55

Strain: lineage4.9

Drug-resistance: HR-TB

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.18 streptomycin
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid
embB 4247448 p.His312Arg missense_variant 0.12 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
gyrA 7949 c.648G>T synonymous_variant 0.96
gyrA 8123 p.Leu274Phe missense_variant 0.95
gyrA 9768 p.Gly823Cys missense_variant 1.0
mshA 575695 c.348C>G synonymous_variant 0.14
mshA 575704 c.357T>C synonymous_variant 0.14
mshA 575705 c.358T>C synonymous_variant 0.14
mshA 575713 c.366G>A synonymous_variant 0.15
mshA 575719 c.372C>T synonymous_variant 0.16
mshA 575734 c.387T>G synonymous_variant 0.14
mshA 575737 c.390T>C synonymous_variant 0.14
mshA 575746 c.399C>G synonymous_variant 0.12
mshA 575752 c.405G>A synonymous_variant 0.15
mshA 575767 c.420G>A synonymous_variant 0.15
mshA 575771 p.Val142Ser missense_variant 0.14
rpoB 760235 c.429T>C synonymous_variant 0.15
rpoB 761852 c.2046C>G synonymous_variant 0.14
rpoB 761858 c.2052G>C synonymous_variant 0.15
rpoB 761864 c.2058G>C synonymous_variant 0.15
rpoB 761873 c.2067A>G synonymous_variant 0.14
rpoB 761948 c.2142G>C synonymous_variant 0.13
rpoB 761999 c.2193G>C synonymous_variant 0.12
rpoB 762114 p.Ile770Val missense_variant 0.16
rpoB 762131 c.2325C>G synonymous_variant 0.16
rpoB 762143 c.2337T>C synonymous_variant 0.15
rpoB 762149 c.2343G>C synonymous_variant 0.14
rpoB 762167 c.2361T>C synonymous_variant 0.15
rpoB 762176 c.2370T>C synonymous_variant 0.14
rpoB 762185 c.2379G>C synonymous_variant 0.17
rpoB 762218 c.2412T>G synonymous_variant 0.13
rpoB 762254 c.2448T>C synonymous_variant 0.12
rpoC 763734 p.Pro122Leu missense_variant 0.91
rpoC 764626 c.1257C>T synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.12
rpoC 764791 c.1422C>G synonymous_variant 0.12
rpoC 764809 c.1440C>T synonymous_variant 0.14
rpoC 764812 c.1443C>G synonymous_variant 0.14
rpoC 764815 c.1446A>G synonymous_variant 0.14
rpoC 764824 c.1455T>C synonymous_variant 0.13
rpoC 764830 c.1461C>G synonymous_variant 0.14
rpoC 764858 c.1489T>C synonymous_variant 0.12
rpoC 764872 c.1503A>G synonymous_variant 0.12
rpoC 764911 c.1542A>G synonymous_variant 0.14
rpoC 765383 p.Met672Leu missense_variant 0.12
rpoC 765404 p.Leu679Val missense_variant 0.12
rpoC 765478 c.2109T>C synonymous_variant 0.15
rpoC 765499 c.2130C>G synonymous_variant 0.12
rpoC 765508 c.2139C>G synonymous_variant 0.12
rpoC 765613 p.His748Gln missense_variant 0.12
rpoC 766522 c.3153C>G synonymous_variant 0.11
rpoC 766528 c.3159T>C synonymous_variant 0.12
rpoC 766543 c.3174C>T synonymous_variant 0.14
rpoC 766549 c.3180G>C synonymous_variant 0.13
rpoC 766573 c.3204T>C synonymous_variant 0.12
rpoC 766583 p.Gly1072Ser missense_variant 0.13
rpoC 766588 c.3219G>A synonymous_variant 0.13
rpoC 766591 c.3222A>G synonymous_variant 0.13
rpoC 766594 c.3225G>C synonymous_variant 0.14
rpoC 766607 p.Ile1080Leu missense_variant 0.12
rpoC 766630 c.3261G>C synonymous_variant 0.14
rpoC 766645 c.3276A>G synonymous_variant 0.14
rpoC 766651 c.3282T>C synonymous_variant 0.12
rpoC 766726 c.3357T>C synonymous_variant 0.12
rpoC 766750 c.3381C>G synonymous_variant 0.12
rpoC 767074 c.3705T>C synonymous_variant 0.12
fbiC 1303695 c.765T>C synonymous_variant 0.15
fbiC 1303791 p.Ile287Met missense_variant 0.17
fbiC 1303818 c.888C>G synonymous_variant 0.18
fbiC 1303836 c.906G>C synonymous_variant 0.12
fbiC 1303846 p.Phe306Val missense_variant 0.12
fbiC 1304646 c.1716T>C synonymous_variant 0.13
fbiC 1304703 c.1773C>G synonymous_variant 0.12
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 1.0
rpsA 1834555 c.1014T>C synonymous_variant 0.11
rpsA 1834558 c.1017C>G synonymous_variant 0.11
tlyA 1918034 p.Val32Ala missense_variant 1.0
katG 2155918 p.Ala65Val missense_variant 1.0
PPE35 2168767 p.Ser616Gly missense_variant 1.0
Rv1979c 2222377 p.Val263Gly missense_variant 1.0
kasA 2518717 c.603C>T synonymous_variant 0.12
kasA 2518723 p.Glu203Asp missense_variant 0.12
ribD 2986993 p.Gly52Val missense_variant 1.0
Rv2752c 3065787 c.405G>C synonymous_variant 1.0
thyA 3074001 c.471C>G synonymous_variant 0.12
thyA 3074004 c.468T>C synonymous_variant 0.12
thyA 3074097 c.375C>G synonymous_variant 0.15
thyA 3074100 c.372T>C synonymous_variant 0.15
thyA 3074106 c.366T>C synonymous_variant 0.15
Rv3083 3448649 p.Arg49Pro missense_variant 1.0
Rv3236c 3613067 p.Val17Gly missense_variant 1.0
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0
rpoA 3877613 p.Ile299Val missense_variant 0.12
rpoA 3877638 c.870T>C synonymous_variant 0.15
rpoA 3877656 c.852T>C synonymous_variant 0.16
rpoA 3877668 c.840A>G synonymous_variant 0.15
rpoA 3877677 p.Ala277Ser missense_variant 0.15
rpoA 3877680 c.828G>C synonymous_variant 0.15
rpoA 3877686 c.822A>G synonymous_variant 0.17
rpoA 3877692 c.816G>C synonymous_variant 0.19
rpoA 3877704 c.804G>T synonymous_variant 0.2
rpoA 3877743 c.765T>C synonymous_variant 0.32
rpoA 3877764 c.744C>G synonymous_variant 0.25
rpoA 3877770 c.738A>G synonymous_variant 0.25
rpoA 3877776 c.732T>C synonymous_variant 0.21
rpoA 3877839 c.669G>C synonymous_variant 0.11
rpoA 3877872 c.636C>T synonymous_variant 0.14
rpoA 3877875 c.633T>G synonymous_variant 0.14
rpoA 3877962 c.546G>T synonymous_variant 0.16
rpoA 3877986 c.522G>C synonymous_variant 0.12
rpoA 3877989 c.519A>G synonymous_variant 0.12
clpC1 4039388 c.1317C>A synonymous_variant 0.12
clpC1 4039391 c.1314T>G synonymous_variant 0.14
clpC1 4039409 c.1296T>C synonymous_variant 0.14
clpC1 4039842 c.862_863insT frameshift_variant 1.0
panD 4044103 p.Ile60Ser missense_variant 1.0
embC 4240780 c.918T>C synonymous_variant 0.13
embC 4240783 c.921G>C synonymous_variant 0.13
embC 4240789 c.927T>C synonymous_variant 0.14
embC 4240819 c.957A>G synonymous_variant 0.13
embC 4240825 c.963G>A synonymous_variant 0.12
embC 4240831 c.969T>G synonymous_variant 0.12
embC 4240867 c.1005T>G synonymous_variant 0.12
embC 4240870 c.1008T>C synonymous_variant 0.12
embC 4240919 c.1057_1059delCTCinsTTG synonymous_variant 0.13
embC 4240936 c.1074A>G synonymous_variant 0.12
embC 4240945 c.1083T>C synonymous_variant 0.12
embC 4240966 c.1104G>T synonymous_variant 0.12
embC 4240979 p.Thr373Gln missense_variant 0.12
embC 4240983 p.Ser374Asn missense_variant 0.12
embC 4240990 c.1128A>G synonymous_variant 0.12
embC 4241017 c.1155T>C synonymous_variant 0.12
embC 4241023 c.1161T>G synonymous_variant 0.12
embC 4241026 c.1164C>G synonymous_variant 0.12
embC 4241035 c.1173G>A synonymous_variant 0.13
embA 4245031 p.Arg600Gln missense_variant 1.0
embB 4247437 c.924A>G synonymous_variant 0.13
embB 4247440 c.927C>G synonymous_variant 0.13
embB 4247464 c.951C>G synonymous_variant 0.14
embB 4247470 c.957T>C synonymous_variant 0.14
embB 4247491 c.978G>C synonymous_variant 0.16
gid 4408218 c.-16G>T upstream_gene_variant 1.0