TB-Profiler result

Run: ERR9119101
Summary

Run ID: ERR9119101

Sample name:

Date: 02-04-2023 09:35:39

Number of reads: 609016

Percentage reads mapped: 19.71

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
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 5385 p.Val49Glu missense_variant 0.22
gyrB 5602 c.363C>T synonymous_variant 0.14
gyrB 5770 c.531C>A synonymous_variant 0.22
gyrB 5851 c.612G>A synonymous_variant 0.15
gyrB 6091 c.852G>A synonymous_variant 0.25
gyrA 6889 c.-413G>T upstream_gene_variant 0.14
gyrA 6941 c.-361C>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8163 p.Ala288Ser missense_variant 0.13
gyrA 9035 c.1734G>T synonymous_variant 0.12
gyrA 9096 p.Leu599Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9549 p.Val750Leu missense_variant 0.14
fgd1 491283 c.506delG frameshift_variant 0.18
mshA 575176 c.-172T>C upstream_gene_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576114 p.Arg256Pro missense_variant 0.33
mshA 576615 p.Arg423Gln missense_variant 0.15
ccsA 620111 p.Glu74Gly missense_variant 0.18
ccsA 620589 c.699G>A synonymous_variant 0.17
ccsA 620856 c.966C>A synonymous_variant 0.14
rpoB 760106 c.300G>A synonymous_variant 0.17
rpoB 760791 p.Glu329* stop_gained 0.14
rpoB 761639 c.1833G>T synonymous_variant 0.13
rpoB 762243 p.Arg813Trp missense_variant 0.18
rpoC 762698 c.-672C>G upstream_gene_variant 0.18
rpoC 762863 c.-507T>C upstream_gene_variant 0.38
rpoB 762872 p.Met1022Ile missense_variant 0.5
rpoB 762878 p.Ile1024Met missense_variant 0.31
rpoB 762879 p.Met1025Leu missense_variant 0.31
rpoC 762899 c.-471G>C upstream_gene_variant 0.54
rpoC 762905 c.-465C>T upstream_gene_variant 0.57
rpoB 762925 p.Thr1040Ile missense_variant 0.52
rpoC 762929 c.-441G>C upstream_gene_variant 0.5
rpoB 762939 p.Met1045Leu missense_variant 0.52
rpoB 762942 p.Ile1046Val missense_variant 0.52
rpoC 762965 c.-405T>C upstream_gene_variant 0.33
rpoC 762980 c.-390T>C upstream_gene_variant 0.23
rpoC 763139 c.-231C>A upstream_gene_variant 0.14
rpoB 763141 p.Pro1112Arg missense_variant 0.14
rpoC 763416 p.Thr16Ile missense_variant 0.17
rpoC 764269 c.900G>A synonymous_variant 0.18
rpoC 764602 c.1233C>T synonymous_variant 0.21
rpoC 764605 c.1236G>C synonymous_variant 0.22
rpoC 764611 c.1242G>T synonymous_variant 0.22
rpoC 764623 c.1254C>G synonymous_variant 0.21
rpoC 764632 c.1263T>C synonymous_variant 0.27
rpoC 764641 c.1272C>T synonymous_variant 0.21
rpoC 764650 c.1281G>T synonymous_variant 0.22
rpoC 764660 p.Val431Thr missense_variant 0.22
rpoC 764665 c.1296C>G synonymous_variant 0.23
rpoC 764668 c.1299C>G synonymous_variant 0.23
rpoC 764672 p.Gln435Glu missense_variant 0.23
rpoC 764677 c.1308C>G synonymous_variant 0.23
rpoC 764687 p.Gln440Glu missense_variant 0.32
rpoC 764695 c.1326T>C synonymous_variant 0.33
rpoC 764705 p.Leu446Lys missense_variant 0.35
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765351 p.Ala661Glu missense_variant 0.12
rpoC 765427 c.2058G>A synonymous_variant 0.2
rpoC 765433 p.Met688Ile missense_variant 0.17
rpoC 765759 p.Asn797Ile missense_variant 0.12
rpoC 766245 p.Gln959Pro missense_variant 0.11
rpoC 766513 c.3144C>T synonymous_variant 0.14
rpoC 766775 p.Arg1136Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775644 p.Arg946Leu missense_variant 0.15
mmpL5 775831 p.Ala884Ser missense_variant 0.12
mmpL5 776146 p.Ala779Ser missense_variant 0.25
mmpL5 776756 c.1725C>T synonymous_variant 0.5
mmpL5 777201 p.Ala427Asp missense_variant 0.15
mmpR5 778247 c.-743G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781796 p.Met79Ile missense_variant 0.13
rpsL 781854 p.Arg99Ser missense_variant 0.4
rplC 800931 c.123G>A synonymous_variant 0.18
rplC 801236 p.Ala143Val missense_variant 0.17
fbiC 1303010 p.Arg27Gln missense_variant 0.15
fbiC 1303600 p.Glu224Lys missense_variant 0.22
fbiC 1303644 c.714G>A synonymous_variant 0.18
fbiC 1303769 p.Ser280Leu missense_variant 0.15
fbiC 1303843 p.Ala305Ser missense_variant 0.2
fbiC 1304722 p.Glu598Lys missense_variant 0.13
fbiC 1304790 c.1860C>A synonymous_variant 0.22
fbiC 1305483 c.2553C>T synonymous_variant 0.14
Rv1258c 1406406 p.Pro312Leu missense_variant 0.18
Rv1258c 1407008 c.333C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.15
rrs 1471877 n.32A>G non_coding_transcript_exon_variant 0.15
rrs 1471884 n.39C>A non_coding_transcript_exon_variant 0.15
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.15
rrs 1471893 n.48T>G non_coding_transcript_exon_variant 0.15
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.14
rrs 1471917 n.72G>A non_coding_transcript_exon_variant 0.14
rrs 1471948 n.103A>G non_coding_transcript_exon_variant 0.17
rrs 1472052 n.207A>G non_coding_transcript_exon_variant 0.4
rrs 1472302 n.457G>A non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.36
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.36
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.36
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.59
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.59
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.82
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.78
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.88
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.88
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 1.0
rrs 1473374 n.1529C>T non_coding_transcript_exon_variant 0.22
rrl 1473715 n.58G>T non_coding_transcript_exon_variant 0.2
rrl 1474277 n.620C>T non_coding_transcript_exon_variant 0.29
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.33
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.33
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.35
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.33
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.38
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.38
rrl 1475575 n.1918C>A non_coding_transcript_exon_variant 0.38
rrl 1475577 n.1920C>G non_coding_transcript_exon_variant 0.38
rrl 1475589 n.1932G>A non_coding_transcript_exon_variant 0.15
rrl 1475684 n.2027G>T non_coding_transcript_exon_variant 0.14
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.2
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.29
rrl 1475894 n.2237C>G non_coding_transcript_exon_variant 0.25
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.22
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.22
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.2
rrl 1476203 n.2546G>T non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.44
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.5
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.75
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.87
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.87
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.8
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.8
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.67
rrl 1476502 n.2845G>T non_coding_transcript_exon_variant 0.29
inhA 1673919 c.-283G>A upstream_gene_variant 0.4
rpsA 1833882 p.Gly114Asp missense_variant 0.25
rpsA 1834557 p.Ala339Val missense_variant 0.13
rpsA 1834626 p.Leu362Pro missense_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917988 p.Ala17Ser missense_variant 0.22
tlyA 1918543 p.Gln202* stop_gained 0.25
ndh 2101790 p.Thr418Lys missense_variant 0.17
ndh 2102024 p.Ala340Glu missense_variant 0.2
ndh 2102247 p.Val266Ile missense_variant 0.14
ndh 2102346 p.Ala233Ser missense_variant 0.18
katG 2155220 c.892T>C synonymous_variant 0.13
katG 2155251 c.861A>G synonymous_variant 0.15
katG 2155434 c.678G>C synonymous_variant 0.13
katG 2155446 c.666G>C synonymous_variant 0.21
katG 2155449 c.663C>G synonymous_variant 0.14
katG 2155742 p.Gly124Cys missense_variant 0.33
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156292 c.-181G>A upstream_gene_variant 0.2
katG 2156554 c.-443G>A upstream_gene_variant 0.25
PPE35 2168258 c.2355G>T synonymous_variant 0.5
PPE35 2168665 c.1947delT frameshift_variant 0.33
PPE35 2169283 p.Arg444Ser missense_variant 0.17
Rv1979c 2221896 c.1269G>T synonymous_variant 0.4
Rv1979c 2221905 c.1260T>C synonymous_variant 0.4
Rv1979c 2222948 p.Arg73Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288989 p.Leu85Met missense_variant 0.14
pncA 2289106 p.Ala46Ser missense_variant 0.13
pncA 2289807 c.-566G>T upstream_gene_variant 0.18
pncA 2290152 c.-911G>T upstream_gene_variant 0.67
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715559 c.-227G>T upstream_gene_variant 0.14
eis 2715574 c.-242T>A upstream_gene_variant 0.12
ahpC 2726055 c.-138G>T upstream_gene_variant 0.12
ahpC 2726116 c.-77T>C upstream_gene_variant 0.15
ahpC 2726512 p.Pro107Leu missense_variant 0.29
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747423 p.Ser59Leu missense_variant 0.14
pepQ 2859932 p.Leu163Met missense_variant 0.12
Rv2752c 3065121 p.Lys357Asn missense_variant 1.0
Rv2752c 3065347 p.Ala282Asp missense_variant 0.22
Rv2752c 3065501 p.Gly231* stop_gained 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073882 p.Gly197Asp missense_variant 0.12
ald 3086646 c.-174G>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339332 p.Ala72Val missense_variant 0.15
fbiD 3339452 p.Val112Glu missense_variant 0.14
fbiD 3339685 p.Asp190Tyr missense_variant 0.12
fbiD 3339728 p.Gly204Glu missense_variant 0.15
fbiD 3339747 c.630G>T synonymous_variant 0.2
Rv3083 3449658 c.1155C>T synonymous_variant 0.18
Rv3083 3449968 p.Ala489Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474104 p.Asp33Val missense_variant 0.2
fprA 3474983 p.Gly326Val missense_variant 0.18
fprA 3475303 p.Ala433Ser missense_variant 0.12
whiB7 3568650 c.30C>A synonymous_variant 0.18
Rv3236c 3612759 p.Gly120Ser missense_variant 0.29
Rv3236c 3613003 c.114G>A synonymous_variant 0.29
fbiB 3641644 p.Ala37Glu missense_variant 0.15
rpoA 3878041 p.Gly156Asp missense_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039934 c.771G>T synonymous_variant 0.14
panD 4044318 c.-37G>T upstream_gene_variant 0.12
embC 4241119 c.1257C>A synonymous_variant 0.12
embC 4241191 c.1329C>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244452 p.Pro407Leu missense_variant 0.15
embA 4244993 c.1761C>T synonymous_variant 0.15
embA 4246201 p.Gln990Leu missense_variant 0.18
embB 4246613 p.Gly34Trp missense_variant 0.29
embB 4246674 p.Ala54Val missense_variant 0.33
embB 4247162 p.Leu217Val missense_variant 0.18
embB 4248628 c.2115C>G synonymous_variant 0.13
embB 4249393 p.Trp960Cys missense_variant 0.14
embB 4249625 p.Gly1038Arg missense_variant 0.14
aftB 4267491 p.Ala449Glu missense_variant 0.15
aftB 4267615 p.Val408Ile missense_variant 0.14
aftB 4269456 c.-620G>A upstream_gene_variant 0.17
ubiA 4269608 p.Arg76Ser missense_variant 0.22
ethA 4326212 p.Arg421Pro missense_variant 0.18
ethA 4326419 p.Ala352Val missense_variant 0.17
ethR 4327721 p.Arg58Lys missense_variant 0.18
ethA 4327767 c.-294C>G upstream_gene_variant 0.14
ethR 4328099 p.Phe184Tyr missense_variant 0.2
ethA 4328422 c.-949G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338678 c.-157G>T upstream_gene_variant 0.17
gid 4407753 p.Met150Ile missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0
Rv2752c 3065039 c.1070_1152delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT frameshift_variant 1.0