TB-Profiler result

Run: SRR13861151
Summary

Run ID: SRR13861151

Sample name:

Date: 03-04-2023 09:24:47

Number of reads: 739881

Percentage reads mapped: 12.34

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 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
rpoB 761131 p.Gly442Glu missense_variant 0.25 rifampicin
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 6148 c.909C>G synonymous_variant 0.16
gyrB 6209 c.970C>T synonymous_variant 0.17
gyrB 6214 c.975G>C synonymous_variant 0.18
gyrB 6217 c.978G>C synonymous_variant 0.19
gyrB 6223 c.984G>C synonymous_variant 0.19
gyrA 6778 c.-524C>T upstream_gene_variant 0.14
gyrA 6793 c.-509T>C upstream_gene_variant 0.15
gyrB 6797 p.Gly520Thr missense_variant 0.15
gyrA 6824 c.-478C>T upstream_gene_variant 0.14
gyrA 8375 c.1074G>C synonymous_variant 0.14
gyrA 8391 p.Tyr364His missense_variant 0.15
gyrA 8399 c.1098T>C synonymous_variant 0.18
gyrA 9502 p.Arg734His missense_variant 1.0
fgd1 491232 c.450T>C synonymous_variant 0.15
fgd1 491241 p.Asp153Glu missense_variant 0.18
fgd1 491244 c.462T>C synonymous_variant 0.21
fgd1 491259 c.477T>C synonymous_variant 0.18
fgd1 491286 c.504G>C synonymous_variant 0.15
fgd1 491292 c.510G>C synonymous_variant 0.15
fgd1 491295 c.513C>G synonymous_variant 0.14
fgd1 491296 p.Val172Ile missense_variant 0.14
fgd1 491331 c.549G>A synonymous_variant 0.15
fgd1 491343 c.561C>G synonymous_variant 0.17
fgd1 491349 c.567T>C synonymous_variant 0.18
ccsA 620331 c.441C>T synonymous_variant 0.13
ccsA 620340 c.450C>G synonymous_variant 0.13
ccsA 620362 p.Ala158Thr missense_variant 0.14
ccsA 620367 c.477T>C synonymous_variant 0.14
ccsA 620373 c.483C>G synonymous_variant 0.15
ccsA 620385 c.495G>C synonymous_variant 0.14
ccsA 620388 c.498A>G synonymous_variant 0.13
ccsA 620412 c.522T>C synonymous_variant 0.13
ccsA 620415 c.525T>C synonymous_variant 0.14
ccsA 620461 p.Val191Ile missense_variant 0.12
ccsA 620703 c.813G>C synonymous_variant 0.15
ccsA 620739 c.849A>G synonymous_variant 0.13
ccsA 620745 c.855G>C synonymous_variant 0.17
ccsA 620778 c.888T>C synonymous_variant 0.15
ccsA 620787 c.897C>G synonymous_variant 0.19
rpoB 759681 c.-126C>T upstream_gene_variant 0.95
rpoB 760130 p.Asp108Glu missense_variant 0.17
rpoB 760139 c.333A>G synonymous_variant 0.17
rpoB 760142 c.336C>G synonymous_variant 0.15
rpoB 760181 c.375T>C synonymous_variant 0.16
rpoB 760184 c.378A>G synonymous_variant 0.15
rpoB 760196 c.390C>G synonymous_variant 0.16
rpoB 760223 c.417T>C synonymous_variant 0.16
rpoB 760235 c.429T>C synonymous_variant 0.17
rpoB 760328 c.522G>C synonymous_variant 0.14
rpoB 760361 c.555T>C synonymous_variant 0.14
rpoB 760376 p.Asp190Glu missense_variant 0.15
rpoB 760424 c.618C>G synonymous_variant 0.14
rpoB 761126 c.1320G>T synonymous_variant 0.25
rpoB 761129 c.1323G>C synonymous_variant 0.25
rpoB 761133 p.Leu443Ile missense_variant 0.25
rpoB 761150 c.1344A>C synonymous_variant 0.24
rpoB 761151 p.Leu449Val missense_variant 0.24
rpoB 761156 c.1350G>C synonymous_variant 0.27
rpoB 761162 c.1356G>C synonymous_variant 0.26
rpoB 761165 c.1359G>C synonymous_variant 0.26
rpoB 761168 c.1362C>G synonymous_variant 0.26
rpoB 761178 p.Ser458Thr missense_variant 0.27
rpoB 761192 c.1386C>G synonymous_variant 0.28
rpoB 761195 c.1389G>C synonymous_variant 0.29
rpoB 761196 p.Leu464Phe missense_variant 0.28
rpoB 761204 c.1398C>T synonymous_variant 0.27
rpoB 761207 c.1401C>T synonymous_variant 0.28
rpoB 761213 c.1407G>A synonymous_variant 0.28
rpoB 761220 p.Ser472Thr missense_variant 0.29
rpoB 761234 c.1428G>C synonymous_variant 0.32
rpoB 761235 p.Met477Val missense_variant 0.32
rpoB 761239 p.Cys478Tyr missense_variant 0.68
rpoB 761792 c.1986T>C synonymous_variant 0.12
rpoB 762362 p.Glu852Asp missense_variant 0.14
rpoC 762395 c.-975G>C upstream_gene_variant 0.14
rpoC 762398 c.-972T>C upstream_gene_variant 0.14
rpoC 762470 c.-900G>C upstream_gene_variant 0.14
rpoC 762860 c.-510G>C upstream_gene_variant 0.16
rpoC 762863 c.-507T>C upstream_gene_variant 0.15
rpoB 762878 p.Ile1024Met missense_variant 0.15
rpoB 762879 p.Met1025Leu missense_variant 0.15
rpoB 762888 p.His1028Asn missense_variant 0.14
rpoB 762911 p.Ile1035Met missense_variant 0.15
rpoC 762920 c.-450C>T upstream_gene_variant 0.14
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.15
rpoB 762942 p.Ile1046Val missense_variant 0.15
rpoC 762962 c.-408C>T upstream_gene_variant 0.14
rpoC 762971 c.-399G>A upstream_gene_variant 0.14
rpoC 762983 c.-387C>T upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.19
rpoC 762995 c.-375G>T upstream_gene_variant 0.19
rpoC 764083 c.714A>G synonymous_variant 0.14
rpoC 764098 c.729A>G synonymous_variant 0.15
rpoC 764101 c.732C>G synonymous_variant 0.15
rpoC 764161 c.792G>C synonymous_variant 0.16
rpoC 764188 c.819A>G synonymous_variant 0.17
rpoC 764195 p.Ser276Gln missense_variant 0.15
rpoC 764203 c.834G>T synonymous_variant 0.16
rpoC 764206 c.837T>C synonymous_variant 0.17
rpoC 764266 c.897T>C synonymous_variant 0.14
rpoC 764405 c.1036A>C synonymous_variant 0.25
rpoC 764431 c.1062G>C synonymous_variant 0.16
rpoC 764434 c.1065A>G synonymous_variant 0.29
rpoC 764446 c.1077T>C synonymous_variant 0.28
rpoC 764449 c.1080G>C synonymous_variant 0.15
rpoC 764455 c.1086G>C synonymous_variant 0.17
rpoC 764458 c.1089G>C synonymous_variant 0.15
rpoC 764461 c.1092A>G synonymous_variant 0.16
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764513 p.Phe382Leu missense_variant 0.14
rpoC 764521 c.1152T>C synonymous_variant 0.26
rpoC 764530 c.1161C>G synonymous_variant 0.21
rpoC 764536 c.1167G>C synonymous_variant 0.19
rpoC 764539 c.1170C>G synonymous_variant 0.22
rpoC 764560 c.1191T>C synonymous_variant 0.16
rpoC 764566 c.1197C>G synonymous_variant 0.16
rpoC 764576 p.Ser403Thr missense_variant 0.12
rpoC 765739 c.2370G>C synonymous_variant 0.13
rpoC 765796 c.2427C>T synonymous_variant 0.16
rpoC 765826 c.2457T>C synonymous_variant 0.19
rpoC 765835 c.2466C>T synonymous_variant 0.19
rpoC 765928 c.2559C>G synonymous_variant 0.15
rpoC 766843 c.3474T>C synonymous_variant 0.17
rpoC 766861 c.3492G>C synonymous_variant 0.19
rpoC 766864 c.3495G>C synonymous_variant 0.19
rpoC 766894 c.3525T>C synonymous_variant 0.18
rpoC 766895 c.3526T>C synonymous_variant 0.18
rpoC 766900 c.3531T>C synonymous_variant 0.18
rpoC 766945 c.3576A>G synonymous_variant 0.19
rpoC 766963 c.3594T>C synonymous_variant 0.18
rpoC 766978 c.3609C>G synonymous_variant 0.14
rpoC 766996 c.3627C>T synonymous_variant 0.15
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.15
rpoC 767014 c.3645G>C synonymous_variant 0.15
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.15
rpoC 767059 c.3690T>G synonymous_variant 0.19
rpoC 767062 c.3693C>A synonymous_variant 0.19
rpoC 767074 c.3705T>C synonymous_variant 0.23
mmpL5 776185 p.Lys766Glu missense_variant 1.0
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0
fbiC 1304634 c.1704C>G synonymous_variant 0.14
fbiC 1304640 c.1710A>C synonymous_variant 0.14
fbiC 1304646 c.1716T>C synonymous_variant 0.14
fbiC 1304715 c.1785G>C synonymous_variant 0.13
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.12
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.12
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.16
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.19
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.17
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.18
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrs 1472865 n.1020C>G non_coding_transcript_exon_variant 0.93
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.38
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.37
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.37
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.37
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.38
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.4
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.4
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.39
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.39
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.38
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.37
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.33
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.34
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.37
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.33
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.35
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.24
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.21
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.18
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.18
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.29
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.31
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.3
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.26
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.26
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.26
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.2
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.16
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.15
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.19
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.22
rrl 1474051 n.394T>C non_coding_transcript_exon_variant 0.25
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.26
rrl 1474056 n.399T>C non_coding_transcript_exon_variant 0.3
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.23
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.23
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.2
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.2
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.2
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.22
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.19
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.16
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.15
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.18
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.14
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 0.15
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.15
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 0.15
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.14
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.32
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.78
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.84
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.84
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.84
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.83
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.85
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.87
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.87
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.87
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.84
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.84
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.84
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.82
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.82
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.79
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.29
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.13
inhA 1674382 p.Leu61Ile missense_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 0.17
inhA 1674498 c.297G>A synonymous_variant 0.17
inhA 1674507 c.306G>C synonymous_variant 0.17
inhA 1674537 c.336C>G synonymous_variant 0.16
inhA 1674542 p.Ala114Glu missense_variant 0.17
inhA 1674549 c.348G>C synonymous_variant 0.19
inhA 1674555 c.354G>A synonymous_variant 0.18
inhA 1674561 c.360C>T synonymous_variant 0.17
inhA 1674564 c.363C>T synonymous_variant 0.17
inhA 1674582 c.381T>C synonymous_variant 0.17
inhA 1674585 c.384T>C synonymous_variant 0.17
inhA 1674589 p.Met130Leu missense_variant 0.17
rpsA 1833727 c.186G>C synonymous_variant 0.13
rpsA 1833799 c.258C>G synonymous_variant 0.19
rpsA 1833811 c.270G>C synonymous_variant 0.16
rpsA 1833838 c.297G>C synonymous_variant 0.16
rpsA 1833841 c.300C>G synonymous_variant 0.15
rpsA 1833847 c.306C>G synonymous_variant 0.16
rpsA 1833856 c.315A>G synonymous_variant 0.16
rpsA 1833862 c.321G>T synonymous_variant 0.16
tlyA 1918063 p.Pro42Ala missense_variant 1.0
ndh 2102985 p.Ile20Val missense_variant 1.0
katG 2155856 p.Thr86Ser missense_variant 1.0
PPE35 2169233 c.1379delT frameshift_variant 1.0
Rv2752c 3065376 c.815delT frameshift_variant 1.0
Rv2752c 3066351 c.-160G>T upstream_gene_variant 0.94
thyX 3067376 c.570G>C synonymous_variant 0.15
thyX 3067391 c.555G>C synonymous_variant 0.15
thyX 3067394 c.552G>C synonymous_variant 0.15
thyX 3067412 c.534C>G synonymous_variant 0.15
thyX 3067445 c.501C>G synonymous_variant 0.15
thyX 3067500 p.Lys149Arg missense_variant 0.14
thyX 3067571 c.375C>T synonymous_variant 0.14
thyX 3067577 p.Glu123Asp missense_variant 0.14
thyX 3067586 c.360C>G synonymous_variant 0.14
thyX 3067652 c.294T>C synonymous_variant 0.12
thyX 3067731 p.Val72Ala missense_variant 0.94
thyX 3067825 p.Arg41Gly missense_variant 1.0
thyA 3073878 c.594G>A synonymous_variant 0.16
thyA 3073892 c.580T>C synonymous_variant 0.17
thyA 3073893 c.579C>G synonymous_variant 0.17
thyA 3073926 c.546G>C synonymous_variant 0.18
thyA 3073929 c.543T>C synonymous_variant 0.18
thyA 3073953 c.519T>C synonymous_variant 0.24
thyA 3073977 c.495A>G synonymous_variant 0.19
thyA 3073989 c.483T>C synonymous_variant 0.19
thyA 3074001 c.471C>G synonymous_variant 0.18
thyA 3074004 c.468T>C synonymous_variant 0.18
thyA 3074010 c.462C>G synonymous_variant 0.18
thyA 3074031 c.441T>C synonymous_variant 0.17
thyA 3074037 c.435C>G synonymous_variant 0.17
thyA 3074056 p.Glu139Pro missense_variant 0.16
thyA 3074076 c.396C>G synonymous_variant 0.17
thyA 3074097 c.375C>G synonymous_variant 0.16
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0
Rv3083 3448707 c.204G>A synonymous_variant 1.0
Rv3083 3449768 p.Thr422Lys missense_variant 1.0
fbiB 3641403 c.-132C>T upstream_gene_variant 1.0
alr 3841257 p.His55Leu missense_variant 1.0
rpoA 3877601 p.Gln303* stop_gained 0.96
rpoA 3877743 c.765T>C synonymous_variant 0.22
rpoA 3877764 c.744C>G synonymous_variant 0.19
rpoA 3877770 c.738A>G synonymous_variant 0.19
rpoA 3877776 c.732T>C synonymous_variant 0.19
rpoA 3877782 c.726T>C synonymous_variant 0.19
rpoA 3877818 c.690A>G synonymous_variant 0.23
rpoA 3877839 c.669G>C synonymous_variant 0.24
rpoA 3877857 c.651G>A synonymous_variant 0.22
rpoA 3877866 c.642G>C synonymous_variant 0.17
rpoA 3877875 c.633T>G synonymous_variant 0.14
rpoA 3877899 p.Ser203Thr missense_variant 0.16
rpoA 3877905 c.603A>G synonymous_variant 0.18
rpoA 3877908 p.Asn200Ser missense_variant 0.19
rpoA 3877953 c.555G>A synonymous_variant 0.13
rpoA 3877962 c.546G>T synonymous_variant 0.13
rpoA 3878298 c.210A>G synonymous_variant 0.14
rpoA 3878313 c.195G>C synonymous_variant 0.13
ddn 3986668 c.-176T>C upstream_gene_variant 1.0
clpC1 4038310 p.Val799Met missense_variant 0.12
clpC1 4038623 c.2082A>G synonymous_variant 0.16
clpC1 4038640 p.Asp689Asn missense_variant 0.14
clpC1 4038661 p.Ser682Thr missense_variant 0.14
clpC1 4038671 c.2034T>C synonymous_variant 0.15
clpC1 4038701 c.2004G>C synonymous_variant 0.18
clpC1 4038704 c.2001T>C synonymous_variant 0.18
clpC1 4038707 c.1998C>G synonymous_variant 0.18
clpC1 4038710 c.1995G>C synonymous_variant 0.18
clpC1 4038851 c.1854G>A synonymous_variant 0.13
clpC1 4038908 c.1797C>G synonymous_variant 0.13
clpC1 4039106 c.1599G>C synonymous_variant 0.16
clpC1 4039112 c.1593C>G synonymous_variant 0.16
embC 4241864 p.Leu668Met missense_variant 1.0
embB 4245557 c.-957G>A upstream_gene_variant 1.0
ethA 4327092 p.Ala128Pro missense_variant 1.0
gid 4408151 p.Leu18Val missense_variant 1.0