TB-Profiler result

Run: SRR023450
Summary

Run ID: SRR023450

Sample name:

Date: 02-04-2023 14:12:03

Number of reads: 3610598

Percentage reads mapped: 72.06

Strain: lineage2.2.1

Drug-resistance: RR-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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
rpoB 761139 p.His445Asp missense_variant 0.96 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.38 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.21 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2288713 p.Thr177Pro missense_variant 0.3 pyrazinamide
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 9304 p.Gly668Asp missense_variant 0.98
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491324 p.Val181Gly missense_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575615 p.Thr90Pro missense_variant 0.33
mshA 575824 c.477T>G synonymous_variant 0.21
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576594 p.Val416Gly missense_variant 0.35
ccsA 620051 p.Val54Gly missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759831 p.Thr9Pro missense_variant 0.27
rpoC 762899 c.-471G>T upstream_gene_variant 0.13
rpoC 762920 c.-450C>T upstream_gene_variant 0.19
rpoC 762929 c.-441G>C upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763570 c.201G>C synonymous_variant 0.15
rpoC 763573 c.204G>C synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.2
rpoC 763622 p.Ala85Ser missense_variant 0.12
rpoC 763627 p.Lys86Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777028 p.Thr485Pro missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
fbiC 1303199 p.Val90Gly missense_variant 0.29
fbiC 1304071 p.Thr381Pro missense_variant 0.32
fbiC 1304212 p.Val428Ile missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417179 p.Thr57Pro missense_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.15
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.16
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.29
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.38
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.32
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.22
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.38
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.27
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.26
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.21
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.17
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.22
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.37
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.36
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.35
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.37
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.37
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.35
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.31
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.25
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.25
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.26
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.26
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.28
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.3
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.44
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.49
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.36
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.22
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.32
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.32
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.27
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.25
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.29
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.24
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.48
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.36
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.15
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.14
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.19
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.24
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.25
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.3
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.35
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.33
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.19
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.16
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.17
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.25
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.17
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.2
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.1
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.2
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.41
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.32
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.32
rrl 1474928 n.1271C>T non_coding_transcript_exon_variant 0.15
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.14
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.18
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.19
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.33
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.35
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.39
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.39
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.41
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.39
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.41
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.38
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.39
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.32
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.28
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.17
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.16
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.19
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.23
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.26
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.36
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.3
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.29
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.39
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.35
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.37
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.28
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.28
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.29
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.27
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.37
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.48
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.32
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
fabG1 1673564 p.Val42Gly missense_variant 0.3
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918058 p.Val40Gly missense_variant 0.46
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169971 c.642T>G synonymous_variant 0.36
PPE35 2169974 c.639T>G synonymous_variant 0.34
Rv1979c 2221889 p.Val426Ile missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289900 c.-659A>C upstream_gene_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.27
ahpC 2726341 p.Val50Gly missense_variant 0.25
pepQ 2859904 p.Val172Gly missense_variant 0.29
ribD 2987255 c.417A>C synonymous_variant 0.21
Rv2752c 3066360 c.-169T>G upstream_gene_variant 0.35
thyA 3073863 c.609T>G synonymous_variant 0.35
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.38
fbiD 3339559 p.Thr148Pro missense_variant 0.28
fbiD 3339616 p.Ser167Pro missense_variant 0.25
fbiD 3339626 p.His170Pro missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612113 p.Glu335Gly missense_variant 0.3
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878580 c.-73A>C upstream_gene_variant 0.27
ddn 3986855 c.12A>C synonymous_variant 0.39
ddn 3986929 p.Tyr29Ser missense_variant 0.24
clpC1 4038250 p.Thr819Pro missense_variant 0.38
clpC1 4038278 c.2427T>G synonymous_variant 0.36
panD 4044471 c.-190T>G upstream_gene_variant 0.5
embC 4239883 c.21A>C synonymous_variant 0.31
embC 4240877 p.Thr339Pro missense_variant 0.3
embC 4241429 p.Phe523Val missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242745 c.-488A>C upstream_gene_variant 0.32
embC 4242822 p.Val987Gly missense_variant 0.35
embA 4242952 c.-281T>G upstream_gene_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243903 p.Leu224Arg missense_variant 0.14
embA 4243963 p.Val244Gly missense_variant 0.35
embA 4244332 p.Val367Gly missense_variant 0.3
embA 4244605 p.Val458Gly missense_variant 0.25
embA 4245102 p.Trp624Gly missense_variant 0.3
embA 4246085 p.Glu951Asp missense_variant 0.98
embB 4247811 p.Leu433Arg missense_variant 0.22
aftB 4267227 p.Val537Gly missense_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326925 p.Ser183Arg missense_variant 0.32
whiB6 4338536 c.-15G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0