TB-Profiler result

Run: SRR13861376
Summary

Run ID: SRR13861376

Sample name:

Date: 03-04-2023 09:30:13

Number of reads: 162237

Percentage reads mapped: 5.41

Strain: lineage4.9

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
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
embB 4247448 p.His312Arg missense_variant 0.22 ethambutol
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 5624 p.Asn129Asp missense_variant 1.0
gyrA 7571 c.270G>C synonymous_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 0.29
gyrA 7595 c.294C>G synonymous_variant 0.33
gyrA 7607 c.306C>G synonymous_variant 0.33
gyrA 7626 c.325C>T synonymous_variant 0.25
gyrA 7631 c.330G>C synonymous_variant 0.25
gyrA 7637 c.336C>G synonymous_variant 0.2
gyrA 7658 c.357A>G synonymous_variant 0.2
gyrA 8111 c.810G>C synonymous_variant 0.2
gyrA 8156 c.855T>C synonymous_variant 0.22
gyrA 8174 c.873C>G synonymous_variant 0.25
gyrA 8177 c.876A>C synonymous_variant 0.25
gyrA 8198 c.897T>C synonymous_variant 0.25
gyrA 8204 c.903C>T synonymous_variant 0.25
gyrA 8207 c.906T>C synonymous_variant 0.25
gyrA 8216 c.915G>A synonymous_variant 0.29
gyrA 8219 c.918T>C synonymous_variant 0.29
gyrA 8225 c.924T>C synonymous_variant 0.29
gyrA 8253 p.Ile318Leu missense_variant 0.33
mshA 575194 c.-154G>T upstream_gene_variant 1.0
rpoB 760907 c.1101_1102insT frameshift_variant 1.0
rpoB 761606 c.1800C>G synonymous_variant 0.25
rpoC 763894 c.525A>G synonymous_variant 0.33
rpoC 764405 c.1036A>C synonymous_variant 0.25
rpoC 764431 c.1062G>C synonymous_variant 0.2
rpoC 764434 c.1065A>G synonymous_variant 0.2
rpoC 764497 c.1128A>G synonymous_variant 0.18
rpoC 764530 c.1161C>G synonymous_variant 0.2
rpoC 764536 c.1167G>C synonymous_variant 0.2
rpoC 764539 c.1170C>G synonymous_variant 0.2
rpoC 764560 c.1191T>C synonymous_variant 0.3
rpoC 764566 c.1197C>G synonymous_variant 0.3
rpoC 764573 c.1204_1206delCTTinsTTG synonymous_variant 0.33
rpoC 764576 c.1207_1208delTCinsAG synonymous_variant 0.33
rpoC 764581 c.1212T>C synonymous_variant 0.33
rpoC 764626 c.1257C>T synonymous_variant 0.5
rpoC 764632 c.1263T>C synonymous_variant 0.67
rpoC 764644 c.1275G>C synonymous_variant 0.6
rpoC 764650 c.1281G>T synonymous_variant 0.6
rpoC 764714 c.1345C>T synonymous_variant 1.0
rpoC 764720 c.1351C>T synonymous_variant 1.0
rpoC 764752 c.1383G>C synonymous_variant 1.0
rpoC 764764 c.1395T>C synonymous_variant 1.0
rpoC 764791 c.1422C>G synonymous_variant 0.75
rpoC 764809 c.1440C>T synonymous_variant 0.67
rpoC 764812 c.1443C>G synonymous_variant 0.67
rpoC 765613 p.His748Gln missense_variant 0.67
rpoC 765625 c.2256C>G synonymous_variant 0.5
mmpL5 775898 c.2583G>A synonymous_variant 0.33
mmpL5 775901 c.2580G>A synonymous_variant 0.33
mmpL5 775904 c.2577G>A synonymous_variant 0.33
mmpL5 775909 p.Leu858Phe missense_variant 0.33
mmpL5 775912 c.2569C>A synonymous_variant 0.33
mmpL5 775916 c.2565T>G synonymous_variant 0.33
mmpL5 775937 p.Ala848Ser missense_variant 0.29
mmpL5 775946 c.2535C>G synonymous_variant 0.29
mmpL5 775955 p.Ile842Met missense_variant 0.33
mmpL5 775966 p.Ala839Ser missense_variant 0.4
mmpL5 775975 c.2506T>C synonymous_variant 0.4
mmpL5 775981 p.Leu834Met missense_variant 0.6
mmpL5 775993 p.Glu830Lys missense_variant 0.4
mmpL5 775997 c.2484T>C synonymous_variant 0.4
mmpL5 776000 p.Leu827Ile missense_variant 0.4
mmpL5 776008 p.His825Tyr missense_variant 0.4
mmpL5 776009 c.2472A>G synonymous_variant 0.6
mmpL5 776015 p.Ile822Met missense_variant 0.4
rpsL 781892 c.333A>G synonymous_variant 0.29
rpsL 781898 c.339A>T synonymous_variant 0.29
rplC 801226 p.Gly140Arg missense_variant 1.0
fbiC 1304893 p.Gly655Ser missense_variant 0.2
fbiC 1304916 c.1986T>C synonymous_variant 0.2
fbiC 1304925 c.1995G>C synonymous_variant 0.22
fbiC 1304928 c.1998T>C synonymous_variant 0.22
fbiC 1304934 c.2004C>G synonymous_variant 0.22
fbiC 1304937 c.2007G>C synonymous_variant 0.22
fbiC 1304940 c.2010A>G synonymous_variant 0.22
fbiC 1304946 c.2016G>C synonymous_variant 0.25
fbiC 1304958 c.2028T>G synonymous_variant 0.25
fbiC 1304991 c.2061G>C synonymous_variant 0.33
embR 1417503 c.-156A>C upstream_gene_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.4
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.4
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.4
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.4
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.4
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.33
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.29
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.29
rrl 1475015 n.1358C>T non_coding_transcript_exon_variant 0.29
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.3
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.3
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.2
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.2
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.22
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.22
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.22
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.22
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.22
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.22
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.25
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.25
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.25
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.25
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.29
rrl 1475976 n.2319A>C non_coding_transcript_exon_variant 0.33
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.4
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.4
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.33
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.33
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.5
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.33
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.33
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.33
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.33
rrl 1476716 n.3059A>T non_coding_transcript_exon_variant 0.5
rrl 1476753 n.3099delG non_coding_transcript_exon_variant 1.0
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
inhA 1674498 c.297G>A synonymous_variant 0.67
inhA 1674507 c.306G>C synonymous_variant 0.67
inhA 1674582 c.381T>C synonymous_variant 0.67
inhA 1674585 c.384T>C synonymous_variant 0.67
inhA 1674589 p.Met130Leu missense_variant 0.67
inhA 1674624 c.423A>C synonymous_variant 0.4
inhA 1674627 c.426T>G synonymous_variant 0.4
inhA 1674630 c.429C>G synonymous_variant 0.4
inhA 1674636 c.435C>G synonymous_variant 0.4
rpsA 1833593 c.53delC frameshift_variant 1.0
rpsA 1834884 p.Gln448Leu missense_variant 1.0
PPE35 2169282 p.Arg444His missense_variant 1.0
ahpC 2725932 c.-261G>A upstream_gene_variant 1.0
folC 2746979 p.Ala207Asp missense_variant 0.29
pepQ 2859739 p.Ala227Gly missense_variant 1.0
pepQ 2860197 c.222T>C synonymous_variant 1.0
Rv3083 3448909 p.Leu136Ile missense_variant 1.0
fprA 3474171 c.165G>C synonymous_variant 0.33
fprA 3474177 c.171C>T synonymous_variant 0.4
fbiA 3640691 p.Asp50Val missense_variant 1.0
fbiA 3641204 p.Gly221Asp missense_variant 1.0
rpoA 3878022 c.486T>C synonymous_variant 0.33
rpoA 3878025 c.483C>T synonymous_variant 0.33
rpoA 3878028 c.480G>C synonymous_variant 0.29
rpoA 3878031 c.477T>C synonymous_variant 0.29
rpoA 3878040 c.468T>C synonymous_variant 0.29
rpoA 3878046 c.462T>C synonymous_variant 0.33
rpoA 3878049 c.459G>C synonymous_variant 0.33
rpoA 3878055 c.453A>G synonymous_variant 0.33
clpC1 4038812 c.1893T>C synonymous_variant 0.25
clpC1 4038815 c.1890G>T synonymous_variant 0.25
clpC1 4038851 c.1854G>A synonymous_variant 0.2
clpC1 4038878 c.1827A>G synonymous_variant 0.2
clpC1 4038908 c.1797C>G synonymous_variant 0.15
clpC1 4038914 c.1791G>C synonymous_variant 0.15
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4039073 c.1632C>G synonymous_variant 0.25
clpC1 4039085 c.1620A>G synonymous_variant 0.25
clpC1 4039090 c.1615C>T synonymous_variant 0.22
clpC1 4039097 c.1608G>C synonymous_variant 0.22
clpC1 4039931 c.774T>C synonymous_variant 0.22
clpC1 4039946 c.759A>T synonymous_variant 0.22
clpC1 4039952 c.753T>C synonymous_variant 0.22
clpC1 4039958 c.747G>C synonymous_variant 0.22
clpC1 4039961 p.Tyr248* stop_gained 0.88
clpC1 4040393 c.312G>C synonymous_variant 0.2
clpC1 4040411 c.294T>C synonymous_variant 0.18
clpC1 4040423 c.282A>G synonymous_variant 0.18
clpC1 4040426 c.279T>C synonymous_variant 0.18
clpC1 4040431 c.274T>C synonymous_variant 0.18
clpC1 4040441 c.264C>G synonymous_variant 0.18
embC 4240818 p.Thr319Arg missense_variant 1.0
embB 4247437 c.924A>G synonymous_variant 0.2
embB 4247440 c.927C>G synonymous_variant 0.22
embB 4247464 c.951C>G synonymous_variant 0.22
embB 4247470 c.957T>C synonymous_variant 0.22
embB 4247491 c.978G>C synonymous_variant 0.25
embB 4247497 c.984T>C synonymous_variant 0.25
embB 4247500 c.987C>G synonymous_variant 0.25
embB 4247512 c.999T>C synonymous_variant 0.29
embB 4248081 c.1569dupG frameshift_variant 1.0
ubiA 4269075 p.Ile253Val missense_variant 0.29
aftB 4269081 c.-245G>C upstream_gene_variant 0.29
ubiA 4269088 p.Ala249Val missense_variant 0.29
ubiA 4269100 p.Gly245Glu missense_variant 0.29
ubiA 4269104 p.Ser244Gly missense_variant 0.29
ubiA 4269106 c.727delT frameshift_variant 0.29
ubiA 4269109 c.723_724delCG frameshift_variant 0.29
ubiA 4269117 p.Glu239Asp missense_variant 0.33
aftB 4269123 c.-287T>C upstream_gene_variant 0.33
ubiA 4269141 p.Leu231Val missense_variant 0.33
aftB 4269144 c.-308C>G upstream_gene_variant 0.33
ubiA 4269149 p.Val229Leu missense_variant 0.33
aftB 4269183 c.-347T>C upstream_gene_variant 0.4
ethA 4327644 c.-171G>A upstream_gene_variant 1.0