TB-Profiler result

Run: ERR4816127
Summary

Run ID: ERR4816127

Sample name:

Date: 01-04-2023 14:15:11

Number of reads: 358784

Percentage reads mapped: 94.7

Strain: lineage1.1

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6929 p.Ala564Pro missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620512 p.Gly208Ser missense_variant 0.15
ccsA 620744 p.Ala285Glu missense_variant 0.13
ccsA 620755 p.Asp289Tyr missense_variant 0.14
rpoB 760591 p.Val262Ala missense_variant 0.29
rpoB 760611 c.805T>C synonymous_variant 0.25
rpoB 760629 c.823C>T synonymous_variant 0.43
rpoB 760646 c.840C>G synonymous_variant 0.38
rpoB 760655 c.849A>G synonymous_variant 0.43
rpoB 760661 c.855A>C synonymous_variant 0.5
rpoB 760670 c.864G>C synonymous_variant 0.75
rpoB 760674 c.868T>C synonymous_variant 0.6
rpoB 760679 c.873A>G synonymous_variant 0.5
rpoB 760683 c.877T>C synonymous_variant 0.5
rpoB 761606 c.1800C>G synonymous_variant 0.5
rpoB 761612 c.1806G>C synonymous_variant 0.5
rpoB 761615 c.1809A>C synonymous_variant 0.5
rpoB 761636 c.1830G>T synonymous_variant 0.75
rpoB 761645 c.1839C>G synonymous_variant 0.5
rpoB 761648 c.1842T>C synonymous_variant 0.5
rpoB 761657 c.1851C>G synonymous_variant 0.43
rpoB 761948 c.2142G>C synonymous_variant 0.18
rpoB 761954 c.2148C>G synonymous_variant 0.18
rpoB 761972 c.2166C>G synonymous_variant 0.29
rpoB 762008 c.2202C>T synonymous_variant 0.4
rpoB 762014 c.2208C>T synonymous_variant 0.67
rpoB 762017 c.2211A>G synonymous_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763158 c.-212C>T upstream_gene_variant 0.22
rpoC 763166 c.-204A>G upstream_gene_variant 0.22
rpoC 763190 c.-180C>T upstream_gene_variant 0.25
rpoC 763202 c.-168A>G upstream_gene_variant 0.25
rpoC 763402 c.33C>G synonymous_variant 0.2
rpoC 763411 c.42T>G synonymous_variant 0.2
rpoC 763414 c.45T>C synonymous_variant 0.2
rpoC 763438 p.Trp23* stop_gained 0.25
rpoC 763441 c.72C>T synonymous_variant 0.25
rpoC 763444 c.75T>C synonymous_variant 0.25
rpoC 763456 c.87A>G synonymous_variant 0.4
rpoC 763853 p.Val162Ile missense_variant 0.67
rpoC 763858 c.489A>G synonymous_variant 0.67
rpoC 763872 p.Gly168Ala missense_variant 0.67
rpoC 763876 p.Glu169Asp missense_variant 0.67
rpoC 763879 c.510A>G synonymous_variant 0.67
rpoC 763888 c.519G>C synonymous_variant 0.67
rpoC 763891 c.522G>C synonymous_variant 0.67
rpoC 763894 c.525A>G synonymous_variant 0.67
rpoC 763900 c.531G>C synonymous_variant 0.5
rpoC 764317 c.948C>T synonymous_variant 0.29
rpoC 764353 c.984G>T synonymous_variant 0.2
rpoC 764365 c.996C>T synonymous_variant 0.25
rpoC 764380 c.1011G>C synonymous_variant 0.22
rpoC 764387 c.1018T>C synonymous_variant 0.22
rpoC 764713 c.1344G>C synonymous_variant 0.33
rpoC 764716 c.1347G>C synonymous_variant 0.33
rpoC 764752 c.1383G>C synonymous_variant 0.29
rpoC 764764 c.1395T>C synonymous_variant 0.25
rpoC 764797 c.1428G>C synonymous_variant 0.5
rpoC 764803 c.1434C>T synonymous_variant 0.5
rpoC 764809 c.1440C>T synonymous_variant 0.5
rpoC 764815 c.1446A>G synonymous_variant 0.4
rpoC 764827 c.1458G>C synonymous_variant 0.33
rpoC 764858 c.1489T>C synonymous_variant 0.43
rpoC 764911 c.1542A>G synonymous_variant 0.38
rpoC 764932 c.1563C>A synonymous_variant 0.5
rpoC 764968 c.1599T>C synonymous_variant 0.33
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766861 c.3492G>T synonymous_variant 0.33
rpoC 766864 c.3495G>C synonymous_variant 0.33
rpoC 766945 c.3576A>G synonymous_variant 0.4
rpoC 766972 c.3603G>C synonymous_variant 0.4
rpoC 766978 c.3609C>A synonymous_variant 0.4
rpoC 766996 c.3627C>T synonymous_variant 0.6
rpoC 767012 c.3643C>T synonymous_variant 0.6
rpoC 767032 c.3663G>T synonymous_variant 0.75
rpoC 767035 c.3666G>T synonymous_variant 0.67
rpoC 767059 c.3690T>G synonymous_variant 0.5
rpoC 767062 c.3693C>A synonymous_variant 0.6
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 781622 c.63C>G synonymous_variant 0.29
rplC 801066 c.258G>A synonymous_variant 0.29
fbiC 1303388 p.Ala153Val missense_variant 0.17
Rv1258c 1406888 c.453C>T synonymous_variant 0.29
Rv1258c 1407201 c.139delG frameshift_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
inhA 1674509 c.311delG frameshift_variant 0.4
inhA 1674601 p.Leu134Ala missense_variant 0.22
inhA 1674624 c.423A>C synonymous_variant 0.29
inhA 1674636 c.435C>G synonymous_variant 0.25
rpsA 1833724 c.183C>G synonymous_variant 0.67
rpsA 1833727 c.186G>C synonymous_variant 0.5
rpsA 1833742 c.201A>G synonymous_variant 0.5
rpsA 1833745 c.204G>C synonymous_variant 0.5
rpsA 1833748 c.207C>G synonymous_variant 0.5
rpsA 1833787 c.246C>G synonymous_variant 0.67
rpsA 1833790 c.249T>C synonymous_variant 0.67
rpsA 1833811 c.270G>T synonymous_variant 0.67
rpsA 1833838 c.297G>C synonymous_variant 0.5
rpsA 1833841 c.300C>G synonymous_variant 0.33
rpsA 1833847 c.306C>G synonymous_variant 0.33
rpsA 1834261 c.720A>G synonymous_variant 0.33
rpsA 1834264 c.723G>C synonymous_variant 0.33
rpsA 1834297 c.756C>T synonymous_variant 0.67
rpsA 1834303 c.762T>G synonymous_variant 0.5
rpsA 1834306 c.765T>C synonymous_variant 0.4
rpsA 1834319 p.Val260Ile missense_variant 0.6
rpsA 1834348 c.807T>C synonymous_variant 0.5
rpsA 1834396 c.855G>C synonymous_variant 0.6
rpsA 1834411 c.870T>C synonymous_variant 0.75
rpsA 1834417 c.876G>C synonymous_variant 0.75
rpsA 1834423 c.882G>C synonymous_variant 0.75
rpsA 1834435 c.894G>C synonymous_variant 0.75
rpsA 1834438 c.897C>G synonymous_variant 0.75
rpsA 1834451 c.910T>C synonymous_variant 0.6
rpsA 1834465 c.924T>C synonymous_variant 0.6
rpsA 1834468 c.927A>G synonymous_variant 0.5
rpsA 1834474 c.933C>G synonymous_variant 0.5
rpsA 1834547 p.Gln336Lys missense_variant 0.25
rpsA 1834753 c.1212T>C synonymous_variant 0.5
rpsA 1834759 c.1218A>C synonymous_variant 0.5
rpsA 1834765 p.Glu408Asp missense_variant 0.6
rpsA 1834775 p.Ala412Thr missense_variant 0.5
rpsA 1834780 c.1239A>G synonymous_variant 0.4
rpsA 1834786 c.1245A>G synonymous_variant 0.4
rpsA 1834789 c.1248T>C synonymous_variant 0.4
rpsA 1834792 c.1251G>C synonymous_variant 0.4
rpsA 1834798 c.1257C>G synonymous_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102218 c.825C>A synonymous_variant 0.4
ndh 2102227 c.816C>T synonymous_variant 0.5
ndh 2102230 c.813G>C synonymous_variant 0.5
ndh 2102233 c.810G>A synonymous_variant 0.5
ndh 2102245 c.798C>G synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156532 c.-421C>A upstream_gene_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289149 c.93C>A synonymous_variant 0.29
pncA 2290105 c.-864G>C upstream_gene_variant 0.4
kasA 2517950 c.-165C>G upstream_gene_variant 0.15
kasA 2517974 c.-141T>C upstream_gene_variant 0.17
kasA 2517989 c.-126T>C upstream_gene_variant 0.25
kasA 2517993 c.-122G>T upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519248 c.1135delG frameshift_variant 0.25
eis 2714571 c.762G>A synonymous_variant 0.5
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746308 p.Arg431Ser missense_variant 0.22
folC 2746321 c.1278A>G synonymous_variant 0.2
folC 2746328 p.Arg424Ala missense_variant 0.29
folC 2746335 p.Gly422Arg missense_variant 0.29
folC 2746336 c.1263C>G synonymous_variant 0.29
folC 2746345 c.1254G>C synonymous_variant 0.25
folC 2746393 c.1206C>G synonymous_variant 0.22
folC 2746451 p.Gly383Ala missense_variant 0.2
folC 2746477 p.Phe374Tyr missense_variant 0.18
folC 2746480 c.1119A>C synonymous_variant 0.18
folC 2746494 c.1103_1104delAT frameshift_variant 0.25
folC 2746498 c.1100_1101insCG frameshift_variant 0.29
folC 2746507 c.1092A>G synonymous_variant 0.29
folC 2746510 c.1089A>G synonymous_variant 0.29
folC 2746516 c.1083T>G synonymous_variant 0.29
folC 2746519 p.Ser360Ala missense_variant 0.29
folC 2746525 c.1074G>C synonymous_variant 0.29
pepQ 2859969 c.450C>T synonymous_variant 0.18
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065689 p.Thr168Ile missense_variant 0.29
thyX 3067316 c.630A>G synonymous_variant 0.11
thyX 3067850 c.96A>C synonymous_variant 0.17
thyX 3067853 c.93C>T synonymous_variant 0.18
thyX 3067869 p.Thr26Ser missense_variant 0.25
thyX 3067874 c.72C>G synonymous_variant 0.27
thyX 3067883 c.63C>G synonymous_variant 0.31
thyX 3067886 c.60A>C synonymous_variant 0.31
thyX 3067889 c.57C>G synonymous_variant 0.29
thyX 3067898 p.Asp16Glu missense_variant 0.31
thyX 3067935 p.Thr4Ile missense_variant 0.17
thyX 3068151 c.-206T>C upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449508 c.1005G>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475315 p.His437Asn missense_variant 0.17
whiB7 3568872 c.-193C>T upstream_gene_variant 0.29
Rv3236c 3613053 p.Gly22Arg missense_variant 0.29
fbiA 3641408 c.868delG frameshift_variant 0.2
rpoA 3877668 c.840A>G synonymous_variant 0.2
rpoA 3877679 p.Ala277Ser missense_variant 0.22
rpoA 3877686 c.822A>G synonymous_variant 0.22
rpoA 3877692 c.816G>C synonymous_variant 0.22
rpoA 3877704 c.804G>T synonymous_variant 0.22
rpoA 3877743 c.765T>C synonymous_variant 0.18
rpoA 3877887 c.621G>C synonymous_variant 0.25
rpoA 3877896 c.612G>C synonymous_variant 0.25
rpoA 3877900 p.Ser203Asn missense_variant 0.22
rpoA 3877905 c.603A>G synonymous_variant 0.2
rpoA 3877908 p.Asn200Ser missense_variant 0.2
rpoA 3877920 c.588G>C synonymous_variant 0.3
rpoA 3877926 c.582G>C synonymous_variant 0.3
rpoA 3877962 c.546G>T synonymous_variant 0.43
rpoA 3877986 c.522G>C synonymous_variant 0.5
rpoA 3877989 c.519A>G synonymous_variant 0.4
rpoA 3878001 c.507A>G synonymous_variant 0.4
clpC1 4039973 p.Asp244Glu missense_variant 0.4
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040675 c.30C>G synonymous_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242886 c.-347G>A upstream_gene_variant 0.13
embA 4242892 c.-341G>C upstream_gene_variant 0.13
embA 4242901 c.-332G>C upstream_gene_variant 0.12
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246347 p.Thr1039Ala missense_variant 0.12
embB 4246727 c.217_218dupTC frameshift_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4266972 p.Gly622Asp missense_variant 0.33
aftB 4268904 c.-68C>T upstream_gene_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269532 p.Leu101Pro missense_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328340 c.-867A>G upstream_gene_variant 0.18
ethA 4328363 c.-890A>G upstream_gene_variant 0.22
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407832 p.Val124Gly missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0