TB-Profiler result

Run: ERR4769446
Summary

Run ID: ERR4769446

Sample name:

Date: 01-04-2023 06:40:54

Number of reads: 57373

Percentage reads mapped: 3.66

Strain: lineage4.9;La1.3

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
La1.3 M.bovis None None 0.06
lineage4 Euro-American LAM;T;S;X;H None 0.82
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760982 c.1176G>T synonymous_variant 1.0
rpoB 760991 c.1185G>A synonymous_variant 0.67
rpoB 761015 c.1209G>C synonymous_variant 0.5
rpoB 761021 c.1215G>C synonymous_variant 0.5
rpoB 761027 c.1221A>G synonymous_variant 0.5
rpoB 761036 c.1230G>C synonymous_variant 0.5
rpoB 761037 c.1231T>C synonymous_variant 0.5
rpoB 761051 c.1245G>T synonymous_variant 0.5
rpoB 761054 c.1248G>C synonymous_variant 0.5
rpoB 761057 c.1251G>C synonymous_variant 0.5
rpoB 761060 c.1254C>G synonymous_variant 0.5
rpoB 761084 c.1278C>G synonymous_variant 0.5
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.5
rpoB 761096 c.1290G>C synonymous_variant 0.5
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.5
rpoB 761102 c.1296A>G synonymous_variant 0.5
rpoB 762086 c.2280G>C synonymous_variant 0.67
rpoC 762995 c.-375G>T upstream_gene_variant 0.67
rpoC 763028 c.-342T>C upstream_gene_variant 0.33
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 0.43
rpoC 763049 c.-321G>A upstream_gene_variant 0.29
rpoC 763053 c.-317T>C upstream_gene_variant 0.25
rpoC 763070 c.-300T>C upstream_gene_variant 0.38
rpoB 763074 p.Thr1090Val missense_variant 0.25
rpoC 763079 c.-291C>G upstream_gene_variant 0.25
rpoC 763085 c.-285C>G upstream_gene_variant 0.38
rpoC 763088 c.-282C>G upstream_gene_variant 0.25
rpoC 763094 c.-276G>C upstream_gene_variant 0.25
rpoC 763115 c.-255T>C upstream_gene_variant 0.33
rpoC 763900 c.531G>C synonymous_variant 1.0
rpoC 763909 c.540C>T synonymous_variant 1.0
rpoC 763921 c.552G>C synonymous_variant 1.0
rpoC 763936 c.567C>G synonymous_variant 1.0
rpoC 763940 p.Ala191Ser missense_variant 1.0
rpoC 763947 p.Ala193Val missense_variant 1.0
rpoC 763951 c.582G>C synonymous_variant 1.0
rpoC 763960 c.591T>C synonymous_variant 1.0
rpoC 763961 p.Arg198Lys missense_variant 1.0
rpoC 763985 p.Arg206Lys missense_variant 1.0
rpoC 763991 p.Ile208Leu missense_variant 0.67
rpoC 763996 c.627T>C synonymous_variant 0.67
rpoC 764005 c.636G>C synonymous_variant 0.67
rpoC 764024 c.655T>C synonymous_variant 0.67
rpoC 764539 c.1170C>G synonymous_variant 0.67
rpoC 764548 c.1179G>C synonymous_variant 0.5
rpoC 764554 c.1185C>T synonymous_variant 0.5
rpoC 764566 c.1197C>G synonymous_variant 0.5
rpoC 764572 c.1203G>C synonymous_variant 0.5
rpoC 764575 c.1206T>G synonymous_variant 0.5
rpoC 764576 c.1207_1209delTCCinsAGT synonymous_variant 0.5
rpoC 764602 c.1233C>T synonymous_variant 0.5
rpoC 764605 c.1236G>T synonymous_variant 0.5
rpoC 764626 c.1257C>T synonymous_variant 0.5
rpoC 764644 c.1275G>C synonymous_variant 0.5
rpoC 764650 c.1281G>T synonymous_variant 0.5
rpoC 764662 c.1293G>C synonymous_variant 0.5
rpoC 764677 c.1308C>G synonymous_variant 0.5
rpoC 764680 c.1311G>A synonymous_variant 0.5
rpoC 764731 c.1362G>A synonymous_variant 0.67
rpoC 764752 c.1383G>C synonymous_variant 1.0
rpoC 764758 c.1389C>G synonymous_variant 1.0
rpoC 764764 c.1395T>C synonymous_variant 1.0
rpoC 765751 c.2382C>T synonymous_variant 1.0
rpoC 767023 c.3654C>T synonymous_variant 0.4
rpoC 767044 c.3675G>C synonymous_variant 0.4
rpoC 767059 c.3690T>C synonymous_variant 0.4
rpoC 767062 c.3693C>A synonymous_variant 0.4
rpoC 767098 c.3729T>C synonymous_variant 0.67
rpoC 767106 p.Asn1246Ile missense_variant 1.0
rpoC 767110 c.3741T>C synonymous_variant 1.0
rpsL 781658 c.99A>G synonymous_variant 0.67
rpsL 781682 c.123T>C synonymous_variant 0.8
rpsL 781700 c.141G>C synonymous_variant 0.8
rpsL 781706 c.147T>G synonymous_variant 0.8
rpsL 781715 c.156T>C synonymous_variant 0.8
rpsL 781718 c.159C>G synonymous_variant 0.8
rpsL 781721 c.162C>T synonymous_variant 0.8
rpsL 781728 c.169T>C synonymous_variant 0.8
rpsL 781733 c.174G>C synonymous_variant 0.8
rpsL 781736 c.177T>C synonymous_variant 0.8
rpsL 781737 p.Gln60Ala missense_variant 0.8
rpsL 781754 c.195G>T synonymous_variant 0.67
rpsL 781763 c.204C>G synonymous_variant 0.5
rpsL 781766 c.207C>T synonymous_variant 0.67
rpsL 781769 c.210G>A synonymous_variant 0.67
rpsL 781802 c.243G>C synonymous_variant 0.6
rplC 800633 c.-176T>C upstream_gene_variant 0.67
rplC 800645 c.-164C>T upstream_gene_variant 0.67
rplC 800648 c.-161A>G upstream_gene_variant 0.67
rplC 800654 c.-155T>C upstream_gene_variant 0.67
rplC 800672 c.-137G>C upstream_gene_variant 1.0
rplC 800690 c.-119C>T upstream_gene_variant 1.0
rplC 800693 c.-116A>G upstream_gene_variant 1.0
rplC 800703 c.-106T>C upstream_gene_variant 1.0
rplC 800715 c.-94A>C upstream_gene_variant 0.67
rplC 800720 c.-89T>C upstream_gene_variant 0.67
rplC 800723 c.-86C>G upstream_gene_variant 0.67
rplC 800735 c.-74C>G upstream_gene_variant 0.67
rplC 800738 c.-71T>G upstream_gene_variant 0.67
rplC 800747 c.-62C>T upstream_gene_variant 0.67
rplC 800762 c.-47T>G upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472580 n.735C>A non_coding_transcript_exon_variant 0.6
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.67
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.67
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 1.0
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 1.0
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.75
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.67
rrs 1472844 n.999C>A non_coding_transcript_exon_variant 0.67
rrs 1472845 n.1000G>A non_coding_transcript_exon_variant 0.67
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 1.0
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 1.0
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 1.0
rrs 1472855 n.1011_1012insGT non_coding_transcript_exon_variant 1.0
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 1.0
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 1.0
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 1.0
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.67
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.67
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.67
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.75
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.75
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.6
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.75
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.75
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.67
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 1.0
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 1.0
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 1.0
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 1.0
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 1.0
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 1.0
rrl 1475481 n.1824C>G non_coding_transcript_exon_variant 1.0
rrl 1475482 n.1825A>G non_coding_transcript_exon_variant 1.0
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 1.0
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 1.0
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 1.0
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 1.0
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 1.0
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 1.0
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 1.0
rrl 1475555 n.1898T>C non_coding_transcript_exon_variant 1.0
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.4
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.4
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.4
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.5
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.5
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.4
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.6
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.4
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.29
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.43
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.4
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.67
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.67
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.5
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.5
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.5
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.5
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.25
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.25
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.43
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.33
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.43
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.57
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.5
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.57
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rpsA 1834261 c.720A>C synonymous_variant 0.4
rpsA 1834264 c.723G>C synonymous_variant 0.4
rpsA 1834279 c.738C>T synonymous_variant 0.4
rpsA 1834298 p.Gln253Glu missense_variant 0.4
rpsA 1834306 c.765T>C synonymous_variant 0.4
rpsA 1834307 p.Asp256Asn missense_variant 0.4
rpsA 1834348 c.807T>C synonymous_variant 0.5
rpsA 1834375 c.834G>C synonymous_variant 0.4
rpsA 1834378 c.837T>C synonymous_variant 0.5
rpsA 1834451 c.910T>C synonymous_variant 0.67
rpsA 1834456 c.915T>G synonymous_variant 0.67
rpsA 1834468 c.927A>G synonymous_variant 0.67
rpsA 1834489 c.948T>C synonymous_variant 1.0
rpsA 1834528 c.987T>C synonymous_variant 0.67
rpsA 1834534 c.993C>G synonymous_variant 0.67
rpsA 1834540 c.999G>C synonymous_variant 0.67
rpsA 1834543 c.1002C>G synonymous_variant 0.67
rpsA 1834546 c.1005T>C synonymous_variant 0.67
rpsA 1834552 c.1011G>C synonymous_variant 0.67
rpsA 1834555 c.1014T>G synonymous_variant 0.67
rpsA 1834557 p.Ala339Val missense_variant 0.67
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038782 c.1923G>C synonymous_variant 0.5
clpC1 4038790 c.1915C>T synonymous_variant 0.5
clpC1 4038795 p.Ser637Thr missense_variant 0.5
clpC1 4039463 c.1242C>G synonymous_variant 0.67
clpC1 4039466 c.1239T>C synonymous_variant 0.67
clpC1 4039469 c.1236T>C synonymous_variant 0.67
clpC1 4039472 c.1233G>C synonymous_variant 0.67
clpC1 4039481 c.1224T>C synonymous_variant 0.5
clpC1 4039484 c.1221T>C synonymous_variant 0.5
clpC1 4039487 c.1218G>C synonymous_variant 0.5
clpC1 4039517 c.1188C>G synonymous_variant 0.5
clpC1 4039556 c.1149G>C synonymous_variant 0.5
clpC1 4039559 c.1146C>G synonymous_variant 0.5
clpC1 4039570 p.Met379Leu missense_variant 0.5
clpC1 4039571 c.1134G>C synonymous_variant 0.5
clpC1 4039574 p.Ala377Gly missense_variant 0.5
clpC1 4039577 c.1128T>C synonymous_variant 0.5
clpC1 4039586 c.1119G>C synonymous_variant 0.6
clpC1 4039589 c.1116G>C synonymous_variant 0.67
clpC1 4039610 c.1095G>C synonymous_variant 0.5
clpC1 4039616 c.1089G>C synonymous_variant 0.5
clpC1 4039622 c.1083C>T synonymous_variant 0.43
clpC1 4039634 p.Glu357Asn missense_variant 0.5
clpC1 4039649 c.1056G>C synonymous_variant 0.5
clpC1 4039652 c.1053G>C synonymous_variant 0.5
clpC1 4039661 c.1044T>C synonymous_variant 0.6
clpC1 4039682 c.1023C>G synonymous_variant 0.67
clpC1 4039694 c.1011G>C synonymous_variant 0.6
clpC1 4039724 c.981A>G synonymous_variant 0.5
clpC1 4039733 c.972G>T synonymous_variant 0.5
clpC1 4039751 c.954A>G synonymous_variant 0.5
clpC1 4039757 c.948A>G synonymous_variant 0.5
clpC1 4039760 c.945T>G synonymous_variant 0.5
clpC1 4039766 c.939T>C synonymous_variant 0.5
clpC1 4039769 c.936C>G synonymous_variant 0.5
clpC1 4039778 c.927A>G synonymous_variant 0.67
clpC1 4039793 c.912C>T synonymous_variant 0.67
clpC1 4039850 c.855T>C synonymous_variant 0.5
clpC1 4039865 c.840T>C synonymous_variant 0.67
clpC1 4039887 p.Leu273Pro missense_variant 0.67
clpC1 4040408 c.297C>T synonymous_variant 0.67
clpC1 4040411 c.294T>C synonymous_variant 0.75
clpC1 4040426 c.279T>C synonymous_variant 1.0
clpC1 4040431 c.274T>C synonymous_variant 1.0
clpC1 4040441 c.264C>G synonymous_variant 1.0
clpC1 4040444 c.261C>G synonymous_variant 1.0
clpC1 4040450 c.255A>G synonymous_variant 1.0
clpC1 4040465 c.240T>C synonymous_variant 1.0
clpC1 4040474 c.231C>T synonymous_variant 1.0
clpC1 4040477 c.228G>T synonymous_variant 1.0
clpC1 4040480 c.225T>C synonymous_variant 1.0
clpC1 4040486 c.219G>C synonymous_variant 1.0
clpC1 4040513 c.192G>A synonymous_variant 1.0
clpC1 4040522 c.183T>C synonymous_variant 1.0
clpC1 4040531 c.174T>C synonymous_variant 1.0
clpC1 4040534 c.171A>G synonymous_variant 1.0
clpC1 4040539 c.166C>T synonymous_variant 0.67
clpC1 4040546 c.159G>T synonymous_variant 1.0
clpC1 4040549 c.154_156delTTGinsCTC synonymous_variant 1.0
clpC1 4040561 c.144A>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408304 c.-102G>A upstream_gene_variant 0.29