TB-Profiler result

Run: SRR13861611
Summary

Run ID: SRR13861611

Sample name:

Date: 03-04-2023 09:36:16

Number of reads: 1012428

Percentage reads mapped: 16.89

Strain: lineage4.9

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 0.98
lineage4.9 Euro-American (H37Rv-like) T1 None 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
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 6190 c.951A>G synonymous_variant 0.15
gyrB 6209 c.970C>T synonymous_variant 0.16
gyrB 6214 c.975G>C synonymous_variant 0.16
gyrB 6217 c.978G>C synonymous_variant 0.16
gyrB 6223 c.984G>C synonymous_variant 0.16
gyrB 6280 c.1041T>C synonymous_variant 0.16
gyrB 6292 c.1053G>C synonymous_variant 0.14
gyrA 7649 c.348C>T synonymous_variant 0.13
gyrA 7652 c.351C>T synonymous_variant 0.13
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 0.13
gyrA 7760 c.459C>T synonymous_variant 0.13
gyrA 8048 c.747C>T synonymous_variant 0.14
gyrA 8054 c.753T>C synonymous_variant 0.14
gyrA 8057 c.756A>G synonymous_variant 0.14
gyrA 8069 c.768T>C synonymous_variant 0.16
gyrA 8078 c.777A>G synonymous_variant 0.14
gyrA 8090 c.789C>G synonymous_variant 0.16
gyrA 8096 c.795T>C synonymous_variant 0.16
gyrA 8099 c.798T>C synonymous_variant 0.18
gyrA 8111 c.810G>C synonymous_variant 0.18
gyrA 8156 c.855T>C synonymous_variant 0.19
gyrA 8168 c.867A>G synonymous_variant 0.19
gyrA 8324 c.1023T>C synonymous_variant 0.14
gyrA 8391 p.Tyr364His missense_variant 0.16
gyrA 8420 c.1119T>C synonymous_variant 0.15
gyrA 8423 c.1122G>C synonymous_variant 0.15
gyrA 8442 c.1141C>T synonymous_variant 0.19
gyrA 8453 c.1152A>C synonymous_variant 0.15
gyrA 8462 c.1161A>G synonymous_variant 0.15
gyrA 8471 c.1170T>C synonymous_variant 0.17
gyrA 8480 c.1179C>T synonymous_variant 0.15
gyrA 8486 c.1185T>C synonymous_variant 0.15
gyrA 8489 c.1188A>G synonymous_variant 0.15
gyrA 8498 c.1197C>T synonymous_variant 0.15
gyrA 8516 c.1215T>C synonymous_variant 0.15
gyrA 8519 c.1218A>C synonymous_variant 0.16
gyrA 8546 c.1245T>C synonymous_variant 0.13
mshA 575623 c.276C>G synonymous_variant 0.14
mshA 575659 c.312A>G synonymous_variant 0.17
mshA 575665 c.318G>C synonymous_variant 0.16
mshA 575704 c.357T>C synonymous_variant 0.15
mshA 575705 c.358T>C synonymous_variant 0.15
mshA 575713 c.366G>A synonymous_variant 0.15
mshA 575719 c.372C>T synonymous_variant 0.15
mshA 575734 c.387T>G synonymous_variant 0.16
mshA 575737 c.390T>C synonymous_variant 0.16
mshA 575746 c.399C>G synonymous_variant 0.17
mshA 575752 c.405G>A synonymous_variant 0.2
mshA 575767 c.420G>A synonymous_variant 0.18
mshA 575771 p.Val142Ser missense_variant 0.16
mshA 575779 c.432A>G synonymous_variant 0.17
rpoB 760130 p.Asp108Glu missense_variant 0.16
rpoB 760139 c.333A>G synonymous_variant 0.16
rpoB 760142 c.336C>G synonymous_variant 0.16
rpoB 760181 c.375T>C synonymous_variant 0.15
rpoB 760184 c.378A>G synonymous_variant 0.15
rpoB 760340 c.534G>C synonymous_variant 0.15
rpoB 760361 c.555T>C synonymous_variant 0.15
rpoB 760475 c.669A>G synonymous_variant 0.21
rpoB 760481 c.675G>C synonymous_variant 0.22
rpoB 760484 c.678A>G synonymous_variant 0.22
rpoB 760514 c.708C>T synonymous_variant 0.19
rpoB 760522 p.Ser239Asn missense_variant 0.18
rpoB 760532 c.726T>C synonymous_variant 0.18
rpoB 760533 p.Val243Thr missense_variant 0.18
rpoB 760547 c.741G>C synonymous_variant 0.17
rpoB 760563 p.Arg253Met missense_variant 0.18
rpoB 760591 p.Val262Ala missense_variant 0.2
rpoB 760611 c.805T>C synonymous_variant 0.17
rpoB 760634 c.828T>C synonymous_variant 0.19
rpoB 760646 c.840C>G synonymous_variant 0.16
rpoB 760655 c.849A>G synonymous_variant 0.17
rpoB 760661 c.855A>C synonymous_variant 0.16
rpoB 760670 c.864G>C synonymous_variant 0.16
rpoB 760674 c.868T>C synonymous_variant 0.16
rpoB 760679 c.873A>G synonymous_variant 0.17
rpoB 760683 c.877T>C synonymous_variant 0.17
rpoB 760718 c.912C>G synonymous_variant 0.15
rpoB 760724 c.918T>C synonymous_variant 0.16
rpoB 760730 c.924T>C synonymous_variant 0.15
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 0.14
rpoB 760946 c.1140A>G synonymous_variant 0.14
rpoB 761222 c.1416G>C synonymous_variant 0.18
rpoB 762083 c.2277T>C synonymous_variant 0.17
rpoB 762086 c.2280G>C synonymous_variant 0.16
rpoB 762131 c.2325C>G synonymous_variant 0.15
rpoB 762143 c.2337T>C synonymous_variant 0.14
rpoC 762698 c.-672C>T upstream_gene_variant 1.0
rpoB 762936 p.Ser1044Thr missense_variant 0.13
rpoB 762958 p.Leu1051Pro missense_variant 0.85
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.15
rpoC 763633 c.264T>C synonymous_variant 0.16
rpoC 763636 c.267T>C synonymous_variant 0.16
rpoC 763642 c.273G>C synonymous_variant 0.16
rpoC 763660 c.291T>G synonymous_variant 0.14
rpoC 763675 c.306C>G synonymous_variant 0.16
rpoC 764521 c.1152T>C synonymous_variant 0.17
rpoC 764714 c.1345C>T synonymous_variant 0.15
rpoC 764720 c.1351C>T synonymous_variant 0.15
rpoC 765319 c.1950A>G synonymous_variant 0.15
rpoC 765326 p.His653Ala missense_variant 0.15
rpoC 765330 p.Ser654Asn missense_variant 0.15
rpoC 765383 p.Met672Leu missense_variant 0.17
rpoC 765404 p.Leu679Val missense_variant 0.14
rpoC 765409 c.2040T>C synonymous_variant 0.15
rpoC 765412 c.2043T>C synonymous_variant 0.15
rpoC 765421 c.2052C>G synonymous_variant 0.14
rpoC 765796 c.2427C>T synonymous_variant 0.15
rpoC 765811 c.2442T>C synonymous_variant 0.17
rpoC 765814 c.2445A>G synonymous_variant 0.17
rpoC 765826 c.2457T>C synonymous_variant 0.21
rpoC 765835 c.2466C>T synonymous_variant 0.17
rpoC 765883 c.2514C>G synonymous_variant 0.17
rpoC 765886 c.2517C>G synonymous_variant 0.17
rpoC 765892 c.2523T>C synonymous_variant 0.17
rpoC 765928 c.2559C>G synonymous_variant 0.2
rpsL 781832 c.273T>C synonymous_variant 0.14
rplC 800771 c.-38C>T upstream_gene_variant 0.17
rplC 800814 c.6A>G synonymous_variant 0.18
rplC 800817 c.9A>T synonymous_variant 0.17
rplC 800937 c.129A>G synonymous_variant 0.15
rplC 800939 p.Arg44His missense_variant 0.15
rplC 800949 c.141T>C synonymous_variant 0.14
rplC 801301 c.493C>A synonymous_variant 0.14
rplC 801312 c.504G>C synonymous_variant 0.22
rplC 801324 c.516T>C synonymous_variant 0.17
rplC 801336 c.528C>G synonymous_variant 0.15
rplC 801339 c.531T>C synonymous_variant 0.15
rplC 801341 p.Leu178Gln missense_variant 0.15
rplC 801348 c.540T>G synonymous_variant 0.14
rplC 801357 c.549T>C synonymous_variant 0.14
fbiC 1302962 p.Ala11Gly missense_variant 1.0
fbiC 1303632 c.702T>G synonymous_variant 0.14
fbiC 1303706 p.Leu259Arg missense_variant 0.9
fbiC 1303836 c.906G>C synonymous_variant 0.21
fbiC 1303845 c.915C>G synonymous_variant 0.21
fbiC 1303846 p.Phe306Val missense_variant 0.21
fbiC 1303854 c.924T>C synonymous_variant 0.2
fbiC 1303860 c.930A>C synonymous_variant 0.19
fbiC 1303881 c.951G>C synonymous_variant 0.18
fbiC 1303884 c.954T>G synonymous_variant 0.17
fbiC 1303911 c.981G>C synonymous_variant 0.17
fbiC 1303914 c.984C>G synonymous_variant 0.2
fbiC 1303920 c.990C>G synonymous_variant 0.19
fbiC 1303923 c.993C>T synonymous_variant 0.19
fbiC 1303929 c.999G>C synonymous_variant 0.19
fbiC 1303947 c.1017T>C synonymous_variant 0.2
fbiC 1303948 p.Gly340Arg missense_variant 0.21
fbiC 1303969 p.Val347Ile missense_variant 0.21
fbiC 1303973 p.Gly348Ala missense_variant 0.21
fbiC 1303995 c.1065C>T synonymous_variant 0.16
fbiC 1304001 c.1071C>G synonymous_variant 0.18
fbiC 1304008 c.1078T>C synonymous_variant 0.19
fbiC 1304034 c.1104A>G synonymous_variant 0.19
fbiC 1304040 c.1110C>G synonymous_variant 0.21
fbiC 1304046 c.1116C>G synonymous_variant 0.16
fbiC 1304049 c.1119T>G synonymous_variant 0.15
fbiC 1305204 c.2274C>T synonymous_variant 0.14
fbiC 1305210 c.2280G>C synonymous_variant 0.14
fbiC 1305222 c.2292C>G synonymous_variant 0.14
fbiC 1305231 c.2301C>G synonymous_variant 0.13
fbiC 1305237 c.2307A>G synonymous_variant 0.13
fbiC 1305384 c.2454G>T synonymous_variant 0.97
Rv1258c 1406724 p.Gln206Leu missense_variant 1.0
embR 1416800 p.Ala183Gly missense_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.17
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.17
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.15
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.19
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.19
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.18
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.18
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.16
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.18
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.18
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.18
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.17
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.16
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.19
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.18
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.19
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.16
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.15
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.22
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.21
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.57
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.69
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.68
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.69
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.74
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.74
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.74
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.72
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.74
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.74
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.71
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.67
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.67
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.66
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
fabG1 1673153 c.-287C>G upstream_gene_variant 1.0
rpsA 1833555 p.Thr5Ser missense_variant 0.96
rpsA 1833667 c.126C>G synonymous_variant 0.13
rpsA 1833742 c.201A>G synonymous_variant 0.15
rpsA 1833745 c.204G>C synonymous_variant 0.15
rpsA 1833787 c.246C>G synonymous_variant 0.19
rpsA 1833790 c.249T>A synonymous_variant 0.19
rpsA 1833799 c.258C>G synonymous_variant 0.19
rpsA 1833811 c.270G>C synonymous_variant 0.15
rpsA 1833838 c.297G>C synonymous_variant 0.14
rpsA 1834073 p.Lys178* stop_gained 0.94
rpsA 1834222 c.681T>C synonymous_variant 0.15
rpsA 1834546 c.1005T>C synonymous_variant 0.15
rpsA 1834555 c.1014T>C synonymous_variant 0.15
rpsA 1834558 c.1017C>G synonymous_variant 0.15
rpsA 1834606 c.1065C>G synonymous_variant 0.19
rpsA 1834609 c.1068T>C synonymous_variant 0.16
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.15
rpsA 1834633 c.1092A>G synonymous_variant 0.19
rpsA 1834639 c.1098T>C synonymous_variant 0.21
rpsA 1834666 c.1125G>C synonymous_variant 0.23
rpsA 1834669 c.1128G>C synonymous_variant 0.24
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.23
rpsA 1834732 c.1191T>C synonymous_variant 0.26
rpsA 1834733 p.Ala398Pro missense_variant 0.25
rpsA 1834753 c.1212T>C synonymous_variant 0.18
rpsA 1834765 c.1224A>G synonymous_variant 0.14
PPE35 2167669 p.Phe982Leu missense_variant 1.0
kasA 2518621 c.507G>A synonymous_variant 0.15
kasA 2518741 c.627G>C synonymous_variant 0.14
kasA 2518768 c.654C>G synonymous_variant 0.14
Rv2752c 3066234 c.-43G>A upstream_gene_variant 1.0
thyX 3067316 c.630A>G synonymous_variant 0.15
thyX 3067325 c.621A>G synonymous_variant 0.15
thyX 3067355 c.591A>C synonymous_variant 0.15
thyX 3067367 c.579G>C synonymous_variant 0.16
thyX 3067718 c.228C>G synonymous_variant 0.2
thyX 3067721 c.225T>C synonymous_variant 0.2
thyX 3067724 c.222G>A synonymous_variant 0.19
thyX 3067727 c.219A>C synonymous_variant 0.19
thyX 3067739 c.207T>C synonymous_variant 0.21
thyX 3067742 c.204A>C synonymous_variant 0.21
thyX 3067761 p.Arg62Lys missense_variant 0.26
thyX 3067765 p.Leu61Ile missense_variant 0.21
thyX 3067781 c.165C>G synonymous_variant 0.22
thyX 3067787 c.159G>A synonymous_variant 0.28
thyX 3067793 c.153T>C synonymous_variant 0.21
thyX 3067799 c.147G>A synonymous_variant 0.2
thyX 3067802 c.144C>G synonymous_variant 0.21
thyX 3067814 c.132T>C synonymous_variant 0.23
thyX 3067826 c.120C>G synonymous_variant 0.17
thyX 3067850 c.96A>C synonymous_variant 0.15
fbiB 3642276 c.743delC frameshift_variant 1.0
rpoA 3877692 c.816G>C synonymous_variant 0.17
rpoA 3877704 c.804G>T synonymous_variant 0.19
rpoA 3877743 c.765T>C synonymous_variant 0.17
rpoA 3877764 c.744C>G synonymous_variant 0.16
rpoA 3877770 c.738A>G synonymous_variant 0.17
rpoA 3877776 c.732T>C synonymous_variant 0.15
rpoA 3877782 c.726T>C synonymous_variant 0.17
rpoA 3877818 c.690A>G synonymous_variant 0.2
rpoA 3877839 c.669G>C synonymous_variant 0.15
rpoA 3877857 c.651G>A synonymous_variant 0.15
rpoA 3877866 c.642G>C synonymous_variant 0.14
rpoA 3877872 c.636C>T synonymous_variant 0.16
rpoA 3877875 c.633T>G synonymous_variant 0.16
rpoA 3877899 p.Ser203Thr missense_variant 0.16
rpoA 3877905 c.603A>G synonymous_variant 0.15
rpoA 3877908 p.Asn200Ser missense_variant 0.15
rpoA 3878111 p.Lys133Gln missense_variant 0.92
clpC1 4038452 c.2253G>C synonymous_variant 0.17
clpC1 4038461 p.Ala748Asp missense_variant 0.14
clpC1 4038530 p.Glu725Asp missense_variant 0.14
clpC1 4038536 c.2169C>T synonymous_variant 0.14
clpC1 4039022 c.1683A>G synonymous_variant 0.14
clpC1 4039121 c.1584T>C synonymous_variant 0.13
clpC1 4039142 c.1563A>G synonymous_variant 0.13
clpC1 4039145 c.1560G>C synonymous_variant 0.13
clpC1 4039622 c.1083C>G synonymous_variant 0.13
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.14
clpC1 4039946 c.759A>T synonymous_variant 0.16
clpC1 4039952 c.753T>C synonymous_variant 0.16
clpC1 4039958 c.747G>C synonymous_variant 0.16
clpC1 4039979 c.726C>G synonymous_variant 0.14
clpC1 4040021 c.684A>C synonymous_variant 0.13
clpC1 4040036 c.669C>G synonymous_variant 0.13
embA 4242703 c.-530C>T upstream_gene_variant 1.0
embB 4249144 c.2631G>C synonymous_variant 1.0