TB-Profiler result

Run: ERR2517528
Summary

Run ID: ERR2517528

Sample name:

Date: 19-10-2023 23:54:45

Number of reads: 2218824

Percentage reads mapped: 90.57

Strain: lineage3

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.462C>T (0.14)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.98
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 0.14 streptomycin
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 6280 c.1041T>C synonymous_variant 0.13
gyrB 6286 c.1047T>C synonymous_variant 0.13
gyrB 6292 c.1053G>C synonymous_variant 0.13
gyrB 6298 c.1059C>T synonymous_variant 0.13
gyrB 6299 c.1060C>T synonymous_variant 0.13
gyrA 6307 c.-995T>G upstream_gene_variant 0.13
gyrA 6325 c.-977C>G upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7760 c.459C>T synonymous_variant 0.13
gyrA 7763 c.462T>C synonymous_variant 0.13
gyrA 7799 c.498A>G synonymous_variant 0.15
gyrA 7835 c.534A>G synonymous_variant 0.17
gyrA 7838 c.537C>G synonymous_variant 0.15
gyrA 7859 c.558A>C synonymous_variant 0.14
gyrA 7865 c.564T>C synonymous_variant 0.14
gyrA 8156 c.855T>C synonymous_variant 0.16
gyrA 8375 c.1074G>C synonymous_variant 0.14
gyrA 8391 p.Tyr364His missense_variant 0.15
gyrA 8399 c.1098T>C synonymous_variant 0.17
gyrA 8420 c.1119T>C synonymous_variant 0.15
gyrA 8423 c.1122G>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9422 c.2121C>T synonymous_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 0.98
fgd1 491232 c.450T>C synonymous_variant 0.15
fgd1 491286 c.504G>C synonymous_variant 0.15
fgd1 491292 c.510G>C synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760181 c.375T>C synonymous_variant 0.15
rpoB 760184 c.378A>G synonymous_variant 0.14
rpoB 760196 c.390C>G synonymous_variant 0.15
rpoB 760223 c.417T>C synonymous_variant 0.15
rpoB 760307 c.501T>C synonymous_variant 0.14
rpoB 760328 c.522G>C synonymous_variant 0.14
rpoB 760406 c.600G>C synonymous_variant 0.14
rpoB 760418 c.612G>C synonymous_variant 0.15
rpoB 760611 c.805T>C synonymous_variant 0.16
rpoB 760634 c.828T>C synonymous_variant 0.19
rpoB 760646 c.840C>G synonymous_variant 0.21
rpoB 760655 c.849A>G synonymous_variant 0.2
rpoB 760661 c.855A>C synonymous_variant 0.19
rpoB 760670 c.864G>C synonymous_variant 0.17
rpoB 760674 c.868T>C synonymous_variant 0.19
rpoB 760679 c.873A>G synonymous_variant 0.19
rpoB 760683 c.877T>C synonymous_variant 0.19
rpoB 760718 c.912C>G synonymous_variant 0.2
rpoB 760721 c.915C>G synonymous_variant 0.18
rpoB 760724 c.918T>C synonymous_variant 0.18
rpoB 760730 c.924T>C synonymous_variant 0.16
rpoB 760919 c.1113C>G synonymous_variant 0.15
rpoB 760925 c.1119T>C synonymous_variant 0.15
rpoB 760928 c.1122G>C synonymous_variant 0.15
rpoB 760934 c.1128C>T synonymous_variant 0.15
rpoB 760946 c.1140A>G synonymous_variant 0.14
rpoB 760970 c.1164G>C synonymous_variant 0.24
rpoB 760982 c.1176G>C synonymous_variant 0.25
rpoB 760985 c.1179G>C synonymous_variant 0.24
rpoB 760991 c.1185G>C synonymous_variant 0.23
rpoB 761015 c.1209G>C synonymous_variant 0.24
rpoB 761021 c.1215G>C synonymous_variant 0.24
rpoB 761027 c.1221A>G synonymous_variant 0.24
rpoB 761036 c.1230G>C synonymous_variant 0.19
rpoB 761037 c.1231T>C synonymous_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoB 761171 c.1365C>T synonymous_variant 0.14
rpoB 761180 c.1374A>C synonymous_variant 0.14
rpoB 761183 c.1377T>G synonymous_variant 0.14
rpoB 761189 c.1383T>G synonymous_variant 0.14
rpoB 761222 c.1416G>C synonymous_variant 0.16
rpoB 761249 c.1443A>G synonymous_variant 0.15
rpoB 761261 c.1455G>T synonymous_variant 0.13
rpoB 762083 c.2277T>C synonymous_variant 0.15
rpoB 762086 c.2280G>C synonymous_variant 0.15
rpoB 762254 c.2448T>C synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.93
rpoC 762929 c.-441G>C upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763486 c.117T>C synonymous_variant 0.16
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.14
rpoC 763570 c.201G>C synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.14
rpoC 763744 c.375G>C synonymous_variant 0.14
rpoC 763945 c.576T>C synonymous_variant 0.18
rpoC 763960 c.591T>C synonymous_variant 0.19
rpoC 763967 p.Gly200Ser missense_variant 0.18
rpoC 764161 c.792G>C synonymous_variant 0.18
rpoC 764181 p.Asp271Gly missense_variant 0.83
rpoC 764188 c.819A>G synonymous_variant 0.16
rpoC 764195 p.Ser276Gln missense_variant 0.16
rpoC 764203 c.834G>T synonymous_variant 0.17
rpoC 764206 c.837T>C synonymous_variant 0.2
rpoC 764257 c.888G>C synonymous_variant 0.19
rpoC 764266 c.897T>C synonymous_variant 0.19
rpoC 764269 c.900G>C synonymous_variant 0.17
rpoC 764278 c.909A>G synonymous_variant 0.14
rpoC 764446 c.1077T>C synonymous_variant 0.14
rpoC 764449 c.1080G>C synonymous_variant 0.14
rpoC 764455 c.1086G>C synonymous_variant 0.15
rpoC 764458 c.1089G>C synonymous_variant 0.16
rpoC 764461 c.1092A>G synonymous_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.28
rpoC 764530 c.1161C>G synonymous_variant 0.27
rpoC 764536 c.1167G>C synonymous_variant 0.26
rpoC 764539 c.1170C>G synonymous_variant 0.26
rpoC 764560 c.1191T>C synonymous_variant 0.26
rpoC 764566 c.1197C>G synonymous_variant 0.24
rpoC 764573 c.1204_1206delCTTinsTTG synonymous_variant 0.21
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.21
rpoC 764581 c.1212T>C synonymous_variant 0.2
rpoC 764626 c.1257C>T synonymous_variant 0.16
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764644 c.1275G>C synonymous_variant 0.13
rpoC 764714 c.1345C>T synonymous_variant 0.14
rpoC 764720 c.1351C>T synonymous_variant 0.14
rpoC 764791 c.1422C>G synonymous_variant 0.14
rpoC 764824 c.1455T>C synonymous_variant 0.14
rpoC 764830 c.1461C>G synonymous_variant 0.15
rpoC 765583 c.2214G>T synonymous_variant 0.14
rpoC 766483 c.3114G>C synonymous_variant 0.14
rpoC 766484 p.Val1039Ile missense_variant 0.14
rpoC 766492 c.3123T>C synonymous_variant 0.16
rpoC 766495 c.3126C>T synonymous_variant 0.16
rpoC 766528 c.3159T>G synonymous_variant 0.17
rpoC 766543 c.3174C>T synonymous_variant 0.16
rpoC 766573 c.3204T>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.14
rpoC 766861 c.3492G>C synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781649 c.90T>C synonymous_variant 0.18
rpsL 781655 c.96T>C synonymous_variant 0.16
rpsL 781682 c.123T>C synonymous_variant 0.15
rplC 800817 c.9A>T synonymous_variant 0.17
rplC 800844 c.36T>C synonymous_variant 0.15
rplC 801222 c.414T>C synonymous_variant 0.18
rplC 801228 c.420T>C synonymous_variant 0.17
fbiC 1303674 c.744C>G synonymous_variant 0.15
fbiC 1303785 c.855G>C synonymous_variant 0.14
fbiC 1303929 c.999G>C synonymous_variant 0.17
fbiC 1303947 c.1017T>C synonymous_variant 0.15
fbiC 1303948 p.Gly340Arg missense_variant 0.16
fbiC 1303981 p.Val351Ile missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.13
rrs 1473290 n.1445delCinsTTT non_coding_transcript_exon_variant 0.15
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.17
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.16
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.22
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.19
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.2
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.2
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.2
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.21
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.14
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.15
rrl 1473981 n.324delGinsTT non_coding_transcript_exon_variant 0.16
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.16
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.16
rrl 1474051 n.394T>C non_coding_transcript_exon_variant 0.15
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.17
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.17
rrl 1474962 n.1306delG non_coding_transcript_exon_variant 0.18
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.23
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.21
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.18
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.21
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.17
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.17
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.16
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.15
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.15
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.14
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.14
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.14
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.14
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.14
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.14
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.13
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.15
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.16
inhA 1674480 c.279T>C synonymous_variant 0.16
inhA 1674486 c.285T>C synonymous_variant 0.16
inhA 1674489 c.288G>C synonymous_variant 0.15
inhA 1674507 c.306G>C synonymous_variant 0.21
inhA 1674537 c.336C>G synonymous_variant 0.25
inhA 1674542 p.Ala114Glu missense_variant 0.26
inhA 1674549 c.348G>C synonymous_variant 0.23
inhA 1674555 c.354G>A synonymous_variant 0.25
inhA 1674561 c.360C>T synonymous_variant 0.28
inhA 1674582 c.381T>C synonymous_variant 0.27
inhA 1674585 c.384T>C synonymous_variant 0.27
inhA 1674589 p.Met130Leu missense_variant 0.28
rpsA 1833595 c.54T>C synonymous_variant 0.14
rpsA 1833619 c.78A>C synonymous_variant 0.14
rpsA 1833862 c.321G>T synonymous_variant 0.14
rpsA 1834240 c.699T>C synonymous_variant 0.13
rpsA 1834249 c.708T>C synonymous_variant 0.14
rpsA 1834264 c.723G>C synonymous_variant 0.15
rpsA 1834297 c.756C>G synonymous_variant 0.19
rpsA 1834303 c.762T>G synonymous_variant 0.16
rpsA 1834306 c.765T>C synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2517947 c.-168C>T upstream_gene_variant 0.14
kasA 2518768 c.654C>G synonymous_variant 0.14
kasA 2518792 c.678C>G synonymous_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067391 c.555G>C synonymous_variant 0.14
thyX 3067412 c.534C>G synonymous_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877962 c.546G>T synonymous_variant 0.16
rpoA 3877986 c.522G>C synonymous_variant 0.17
rpoA 3878094 c.414C>G synonymous_variant 0.14
rpoA 3878100 c.408C>G synonymous_variant 0.14
rpoA 3878142 p.Gly122Glu missense_variant 0.14
rpoA 3878217 c.291A>G synonymous_variant 0.16
rpoA 3878220 c.288C>T synonymous_variant 0.18
rpoA 3878271 c.237T>C synonymous_variant 0.15
rpoA 3878396 c.112C>T synonymous_variant 0.15
rpoA 3878436 c.72A>G synonymous_variant 0.18
rpoA 3878442 c.66G>C synonymous_variant 0.16
rpoA 3878454 c.54A>C synonymous_variant 0.15
rpoA 3878472 p.Asp12Glu missense_variant 0.18
rpoA 3878490 c.18C>A synonymous_variant 0.12
clpC1 4038812 c.1893T>C synonymous_variant 0.15
clpC1 4038815 c.1890G>T synonymous_variant 0.15
clpC1 4039169 p.Glu512Asp missense_variant 0.15
clpC1 4039172 c.1533A>G synonymous_variant 0.15
clpC1 4039178 c.1527G>C synonymous_variant 0.15
clpC1 4039183 c.1522T>C synonymous_variant 0.15
clpC1 4039187 c.1518G>C synonymous_variant 0.16
clpC1 4039190 c.1515C>G synonymous_variant 0.14
clpC1 4039208 c.1497C>G synonymous_variant 0.15
clpC1 4040273 c.432T>C synonymous_variant 0.13
clpC1 4040354 c.351A>G synonymous_variant 0.22
clpC1 4040363 c.342A>C synonymous_variant 0.21
clpC1 4040369 c.336C>G synonymous_variant 0.21
clpC1 4040380 c.325T>C synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embA 4244454 p.Ala408Ser missense_variant 1.0
embB 4245807 c.-707_-705delTTAinsCTG upstream_gene_variant 0.15
embA 4245820 p.Ser863Thr missense_variant 0.16
embB 4247554 c.1041T>C synonymous_variant 0.14
embB 4248007 c.1494C>G synonymous_variant 0.15
embB 4248011 p.Ser500Ala missense_variant 0.15
embB 4248035 p.Val508Ile missense_variant 0.18
embB 4248041 p.Ala510Thr missense_variant 0.17
embB 4248044 p.Lys511Ala missense_variant 0.17
embB 4248052 c.1539G>A synonymous_variant 0.17
embB 4248055 c.1542G>C synonymous_variant 0.17
embB 4248064 c.1551G>C synonymous_variant 0.17
embB 4248070 c.1557T>C synonymous_variant 0.15
embB 4248085 c.1572T>C synonymous_variant 0.16
embB 4248095 c.1582_1584delCTCinsTTG synonymous_variant 0.14
embB 4248118 c.1605T>C synonymous_variant 0.15
embB 4248127 c.1614G>C synonymous_variant 0.17
embB 4248133 c.1620C>G synonymous_variant 0.15
embB 4248142 c.1629T>C synonymous_variant 0.15
embB 4248206 p.Ser565Gly missense_variant 0.14
embB 4248220 c.1707A>G synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0