TB-Profiler result

Run: SRR1172987
Summary

Run ID: SRR1172987

Sample name:

Date: 03-04-2023 03:14:21

Number of reads: 169824

Percentage reads mapped: 13.65

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
lineage4.9 Euro-American (H37Rv-like) T1 None 0.8
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 1472644 n.799C>T non_coding_transcript_exon_variant 0.8 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>G upstream_gene_variant 1.0 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8672 c.1371A>G synonymous_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9489 p.Gly730Cys missense_variant 1.0
gyrA 9764 p.Glu821Asp missense_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 0.8
rpoB 760060 p.Tyr85Leu missense_variant 0.67
rpoB 760067 c.261G>C synonymous_variant 0.4
rpoB 760070 c.264T>G synonymous_variant 0.4
rpoB 760091 c.285G>C synonymous_variant 0.33
rpoB 760101 c.295T>C synonymous_variant 0.33
rpoB 760112 c.306T>C synonymous_variant 0.33
rpoB 760118 c.312T>G synonymous_variant 0.5
rpoB 760121 c.315T>C synonymous_variant 0.5
rpoB 760130 p.Asp108Glu missense_variant 0.5
rpoB 762233 c.2427G>C synonymous_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.75
rpoC 762920 c.-450C>T upstream_gene_variant 0.4
rpoC 762929 c.-441G>T upstream_gene_variant 0.67
rpoC 762932 c.-438G>T upstream_gene_variant 0.6
rpoC 762938 c.-432G>C upstream_gene_variant 0.33
rpoC 762944 c.-426C>T upstream_gene_variant 0.33
rpoC 762962 c.-408C>T upstream_gene_variant 0.4
rpoC 762971 c.-399G>C upstream_gene_variant 0.4
rpoC 763053 c.-317T>C upstream_gene_variant 0.67
rpoC 763067 c.-303C>G upstream_gene_variant 0.4
rpoC 763070 c.-300T>C upstream_gene_variant 0.4
rpoB 763074 p.Thr1090Val missense_variant 0.4
rpoC 763085 c.-285C>G upstream_gene_variant 0.33
rpoC 763744 c.375G>C synonymous_variant 0.5
rpoC 765404 p.Leu679Val missense_variant 0.5
rpoC 765409 c.2040T>C synonymous_variant 0.33
rpoC 765451 c.2082C>A synonymous_variant 0.25
rpoC 765478 c.2109T>C synonymous_variant 0.33
rpoC 765499 c.2130C>G synonymous_variant 0.6
rpoC 765529 c.2160C>T synonymous_variant 0.75
rpoC 765541 c.2172C>G synonymous_variant 1.0
rpoC 766378 c.3009C>T synonymous_variant 0.5
rpoC 766381 c.3012C>T synonymous_variant 0.4
rpoC 766384 c.3015A>G synonymous_variant 0.4
rpoC 766387 c.3018C>G synonymous_variant 0.4
rpoC 766408 c.3039C>T synonymous_variant 0.5
rpoC 766411 c.3042C>G synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777094 p.Leu463Val missense_variant 1.0
mmpL5 777751 p.Arg244Cys missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800814 c.6A>G synonymous_variant 0.29
rplC 800817 c.9A>T synonymous_variant 0.29
fbiC 1304937 c.2007G>C synonymous_variant 0.5
fbiC 1304958 c.2028T>G synonymous_variant 0.5
rrs 1472069 n.224G>A non_coding_transcript_exon_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 1.0
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.93
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.9
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.6
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.75
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.6
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.83
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.83
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.83
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.92
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.93
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.93
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.93
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.93
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 1.0
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 1.0
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.5
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.4
rrs 1472874 n.1029C>T non_coding_transcript_exon_variant 0.43
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.43
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.57
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.67
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472974 n.1129A>T non_coding_transcript_exon_variant 1.0
rrs 1472977 n.1133dupT non_coding_transcript_exon_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.8
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.67
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.44
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.33
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.6
rrs 1473346 n.1501G>C non_coding_transcript_exon_variant 0.57
rrl 1473697 n.40C>G non_coding_transcript_exon_variant 0.25
rrl 1473698 n.41G>C non_coding_transcript_exon_variant 0.29
rrl 1473699 n.42A>T non_coding_transcript_exon_variant 0.29
rrl 1473718 n.61G>A non_coding_transcript_exon_variant 0.33
rrl 1473840 n.183A>T non_coding_transcript_exon_variant 0.5
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.5
rrl 1473884 n.227C>T non_coding_transcript_exon_variant 0.5
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.5
rrl 1473889 n.232G>A non_coding_transcript_exon_variant 0.5
rrl 1473896 n.239C>T non_coding_transcript_exon_variant 0.5
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.57
rrl 1473911 n.254G>A non_coding_transcript_exon_variant 0.4
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.67
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.67
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.67
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.43
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.67
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.8
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>T non_coding_transcript_exon_variant 1.0
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.75
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.67
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.67
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 1.0
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.67
rrl 1474527 n.870T>G non_coding_transcript_exon_variant 0.5
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.8
rrl 1474542 n.885A>C non_coding_transcript_exon_variant 0.86
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.67
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.67
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.8
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.83
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.83
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.83
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.83
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.86
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.86
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.88
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.88
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.8
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.8
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.5
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.5
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.5
rrl 1475562 n.1905C>T non_coding_transcript_exon_variant 0.4
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.5
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.5
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.5
rrl 1475713 n.2056C>T non_coding_transcript_exon_variant 0.33
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.5
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.67
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.88
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.88
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.88
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.86
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.86
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.88
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 1.0
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 1.0
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 1.0
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 1.0
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 1.0
rrl 1476080 n.2423T>G non_coding_transcript_exon_variant 0.67
rrl 1476085 n.2428G>A non_coding_transcript_exon_variant 1.0
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.6
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.83
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.75
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.78
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.78
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.78
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.88
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.88
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.86
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 1.0
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 1.0
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.88
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.7
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.7
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.5
rpsA 1834096 c.555G>C synonymous_variant 0.2
rpsA 1834099 c.558C>G synonymous_variant 0.2
rpsA 1834102 c.561T>C synonymous_variant 0.3
rpsA 1834105 c.564C>G synonymous_variant 0.25
rpsA 1834108 c.567C>G synonymous_variant 0.25
rpsA 1834123 c.582C>G synonymous_variant 0.33
rpsA 1834261 c.720A>G synonymous_variant 0.67
rpsA 1834264 c.723G>C synonymous_variant 0.67
rpsA 1834303 c.762T>C synonymous_variant 0.67
rpsA 1834306 c.765T>C synonymous_variant 0.67
rpsA 1834510 c.969C>T synonymous_variant 0.67
rpsA 1834513 c.972C>G synonymous_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917987 c.48G>A synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2168715 p.Gln633Pro missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
kasA 2518093 c.-22C>A upstream_gene_variant 0.4
kasA 2518162 c.48G>A synonymous_variant 0.29
kasA 2518174 c.60A>G synonymous_variant 0.33
kasA 2518754 p.Arg214Trp missense_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747355 p.Val82Ile missense_variant 0.67
folC 2747359 c.240C>G synonymous_variant 0.67
folC 2747362 c.237G>C synonymous_variant 0.67
folC 2747394 p.Ile69Val missense_variant 0.5
folC 2747395 c.204T>C synonymous_variant 0.5
Rv2752c 3066118 p.Asn25Ser missense_variant 0.29
thyX 3067349 c.597G>C synonymous_variant 0.67
thyX 3067355 c.591A>C synonymous_variant 0.67
thyA 3074439 c.33G>T synonymous_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087817 p.Cys333Phe missense_variant 0.29
Rv3083 3449029 p.Ser176Ala missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568670 c.10C>T synonymous_variant 1.0
rpoA 3878698 c.-191A>G upstream_gene_variant 1.0
clpC1 4038596 c.2109A>G synonymous_variant 0.6
clpC1 4038623 c.2082A>G synonymous_variant 0.67
clpC1 4038812 c.1893T>C synonymous_variant 0.67
clpC1 4038845 c.1860G>C synonymous_variant 1.0
clpC1 4038951 p.Phe585Cys missense_variant 0.29
clpC1 4038953 c.1752A>G synonymous_variant 0.29
clpC1 4039991 c.714G>C synonymous_variant 0.4
embC 4241140 c.1278A>G synonymous_variant 0.4
embC 4241146 c.1284C>G synonymous_variant 0.4
embC 4241170 c.1308G>C synonymous_variant 0.4
embC 4241173 c.1311C>T synonymous_variant 0.4
embC 4241179 c.1317G>A synonymous_variant 0.4
embC 4241203 c.1341T>C synonymous_variant 0.33
embC 4241206 c.1344G>C synonymous_variant 0.4
embC 4241218 c.1356G>C synonymous_variant 0.4
embC 4241479 c.1617C>G synonymous_variant 0.4
embC 4241480 c.1618T>C synonymous_variant 0.4
embC 4241488 c.1626G>C synonymous_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245101 c.1869G>C synonymous_variant 0.5
embA 4245137 c.1905T>C synonymous_variant 0.5
embB 4246055 c.-459T>C upstream_gene_variant 0.22
embB 4246064 c.-450T>C upstream_gene_variant 0.22
embA 4246080 p.Pro950Ser missense_variant 0.22
embB 4246088 c.-426A>G upstream_gene_variant 0.22
embB 4247655 p.Lys381Thr missense_variant 0.4
aftB 4269390 c.-554G>T upstream_gene_variant 0.67
whiB6 4338262 p.Ala87Glu missense_variant 0.5
whiB6 4338371 p.Thr51Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 1.0