TB-Profiler result

Run: SRR3675503
Summary

Run ID: SRR3675503

Sample name:

Date: 04-04-2023 05:30:56

Number of reads: 14842

Percentage reads mapped: 6.93

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 0.99
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
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 7442 c.141G>C synonymous_variant 1.0
gyrA 7451 c.150C>G synonymous_variant 1.0
gyrA 7457 c.156T>C synonymous_variant 1.0
gyrA 7475 c.174A>G synonymous_variant 1.0
gyrA 7480 p.Phe60Tyr missense_variant 1.0
gyrA 7484 c.183T>C synonymous_variant 1.0
gyrA 7490 c.189C>G synonymous_variant 1.0
gyrA 7523 c.222C>G synonymous_variant 1.0
gyrA 7532 c.231T>G synonymous_variant 1.0
gyrA 8987 c.1686C>G synonymous_variant 1.0
gyrA 8990 c.1689C>G synonymous_variant 1.0
gyrA 8996 c.1695T>C synonymous_variant 1.0
gyrA 8998 p.Leu566Trp missense_variant 1.0
gyrA 9017 c.1716C>G synonymous_variant 1.0
gyrA 9056 c.1755C>G synonymous_variant 1.0
gyrA 9062 c.1761C>G synonymous_variant 1.0
gyrA 9068 c.1767G>C synonymous_variant 1.0
gyrA 9071 c.1770G>C synonymous_variant 1.0
gyrA 9080 c.1779G>T synonymous_variant 1.0
gyrA 9089 c.1788G>C synonymous_variant 1.0
gyrA 9099 c.1798_1800delTTAinsCTG synonymous_variant 1.0
gyrA 9104 c.1803C>G synonymous_variant 1.0
fgd1 491259 c.477T>C synonymous_variant 1.0
fgd1 491283 p.Asp167Glu missense_variant 1.0
fgd1 491286 c.504G>C synonymous_variant 1.0
fgd1 491289 c.507C>G synonymous_variant 1.0
fgd1 491292 c.510G>C synonymous_variant 1.0
fgd1 491295 c.513C>G synonymous_variant 1.0
fgd1 491296 p.Val172Ile missense_variant 1.0
fgd1 491302 p.Ile174Val missense_variant 1.0
fgd1 491307 c.525C>G synonymous_variant 1.0
fgd1 491313 c.531C>G synonymous_variant 1.0
fgd1 491319 c.537G>C synonymous_variant 1.0
fgd1 491325 c.543G>C synonymous_variant 1.0
fgd1 491337 c.555C>G synonymous_variant 1.0
fgd1 491340 c.558C>G synonymous_variant 1.0
fgd1 491349 c.567T>C synonymous_variant 1.0
fgd1 491364 c.582T>C synonymous_variant 1.0
fgd1 491367 c.585G>C synonymous_variant 1.0
mshA 575659 c.312A>G synonymous_variant 1.0
mshA 575662 c.315C>G synonymous_variant 1.0
mshA 575665 c.318G>A synonymous_variant 1.0
mshA 575674 c.327G>C synonymous_variant 1.0
mshA 575695 c.348C>G synonymous_variant 1.0
mshA 575701 c.354G>A synonymous_variant 1.0
mshA 575704 c.357T>G synonymous_variant 1.0
mshA 575705 c.358T>C synonymous_variant 1.0
mshA 575713 c.366G>A synonymous_variant 1.0
mshA 575719 c.372C>T synonymous_variant 1.0
mshA 575734 c.387T>G synonymous_variant 1.0
mshA 575737 c.390T>C synonymous_variant 1.0
ccsA 620295 c.405G>T synonymous_variant 1.0
ccsA 620298 c.408G>C synonymous_variant 1.0
ccsA 620310 c.420C>T synonymous_variant 1.0
ccsA 620317 p.Val143Leu missense_variant 1.0
ccsA 620340 c.450C>G synonymous_variant 1.0
ccsA 620346 c.456C>G synonymous_variant 1.0
ccsA 620362 p.Ala158Thr missense_variant 1.0
ccsA 620367 c.477T>C synonymous_variant 1.0
ccsA 620373 c.483C>G synonymous_variant 1.0
ccsA 620376 c.486G>C synonymous_variant 1.0
ccsA 620385 c.495G>C synonymous_variant 1.0
ccsA 620388 c.498A>G synonymous_variant 1.0
ccsA 620389 c.499C>T synonymous_variant 1.0
ccsA 620412 c.522T>C synonymous_variant 1.0
ccsA 620415 c.525T>C synonymous_variant 1.0
ccsA 620421 c.531G>C synonymous_variant 1.0
rpoB 760196 c.390C>G synonymous_variant 1.0
rpoB 760223 c.417T>C synonymous_variant 1.0
rpoB 760235 c.429T>C synonymous_variant 1.0
rpoB 760283 c.477G>C synonymous_variant 1.0
rpoB 760298 c.492G>C synonymous_variant 1.0
rpoB 760307 c.501T>C synonymous_variant 1.0
rpoB 760310 c.504G>C synonymous_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 1.0
rpoB 761727 p.Ser641Gly missense_variant 1.0
rpoB 761728 c.1923dupC frameshift_variant 1.0
rpoB 761732 c.1926C>G synonymous_variant 1.0
rpoB 761735 c.1929C>G synonymous_variant 1.0
rpoB 761747 c.1941G>C synonymous_variant 1.0
rpoB 761750 c.1944G>C synonymous_variant 1.0
rpoB 761765 c.1959T>C synonymous_variant 1.0
rpoB 761772 p.His656Ala missense_variant 1.0
rpoB 761778 p.Asn658Asp missense_variant 1.0
rpoB 761791 p.Arg662His missense_variant 1.0
rpoB 762114 p.Ile770Val missense_variant 1.0
rpoB 762131 c.2325C>G synonymous_variant 1.0
rpoB 762140 c.2334G>C synonymous_variant 1.0
rpoB 762143 c.2337T>C synonymous_variant 1.0
rpoB 762149 c.2343G>C synonymous_variant 1.0
rpoB 762254 c.2448T>G synonymous_variant 1.0
rpoC 762398 c.-972T>C upstream_gene_variant 1.0
rpoC 763013 c.-357C>G upstream_gene_variant 1.0
rpoC 763028 c.-342T>C upstream_gene_variant 1.0
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 1.0
rpoC 763070 c.-300T>C upstream_gene_variant 1.0
rpoC 764752 c.1383G>C synonymous_variant 1.0
rpoC 764827 c.1458G>C synonymous_variant 1.0
rpoC 764858 c.1489T>C synonymous_variant 1.0
rpoC 764888 c.1519T>C synonymous_variant 1.0
rpoC 764911 c.1542A>G synonymous_variant 1.0
rpoC 764932 c.1563C>A synonymous_variant 1.0
rpoC 764948 c.1579T>C synonymous_variant 1.0
rpoC 764968 c.1599T>C synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765019 c.1650A>G synonymous_variant 1.0
rpoC 765034 c.1665T>C synonymous_variant 1.0
rpoC 765326 p.His653Ala missense_variant 1.0
rpoC 765330 p.Ser654Asn missense_variant 1.0
rpoC 765346 c.1977C>G synonymous_variant 1.0
rpoC 765349 c.1980T>C synonymous_variant 1.0
rpoC 765352 c.1983G>C synonymous_variant 1.0
rpoC 767059 c.3690T>G synonymous_variant 1.0
rpoC 767062 c.3693C>A synonymous_variant 1.0
rplC 801309 c.501C>G synonymous_variant 1.0
fbiC 1303695 c.765T>C synonymous_variant 1.0
fbiC 1303704 c.774T>C synonymous_variant 1.0
fbiC 1303708 c.778T>C synonymous_variant 1.0
fbiC 1303728 c.798G>A synonymous_variant 1.0
fbiC 1303731 c.801A>C synonymous_variant 1.0
fbiC 1303732 p.Ser268Ala missense_variant 1.0
fbiC 1303736 p.Glu269Val missense_variant 1.0
fbiC 1303746 c.816T>C synonymous_variant 1.0
fbiC 1303749 c.819G>C synonymous_variant 1.0
fbiC 1303752 c.822A>G synonymous_variant 1.0
fbiC 1303755 c.825T>C synonymous_variant 1.0
fbiC 1303761 c.831T>C synonymous_variant 1.0
fbiC 1303785 c.855G>C synonymous_variant 1.0
fbiC 1303789 p.Ile287Val missense_variant 1.0
fbiC 1303797 c.867A>G synonymous_variant 1.0
fbiC 1303818 c.888C>G synonymous_variant 1.0
fbiC 1303827 c.897A>G synonymous_variant 1.0
atpE 1460852 c.-193C>G upstream_gene_variant 1.0
atpE 1460855 c.-190T>C upstream_gene_variant 1.0
atpE 1460858 c.-187C>G upstream_gene_variant 1.0
atpE 1460861 c.-184C>G upstream_gene_variant 1.0
atpE 1460882 c.-163T>C upstream_gene_variant 1.0
atpE 1460894 c.-151A>G upstream_gene_variant 1.0
atpE 1460897 c.-148A>C upstream_gene_variant 1.0
atpE 1460900 c.-145T>C upstream_gene_variant 1.0
rrs 1472518 n.673G>A non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 1.0
rrs 1472560 n.715G>T non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.8
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.9
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.9
rrs 1472677 n.833_834delTT non_coding_transcript_exon_variant 0.75
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.75
rrs 1472683 n.839_842delGGGA non_coding_transcript_exon_variant 0.75
rrs 1472690 n.845C>G non_coding_transcript_exon_variant 0.57
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.62
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.56
rrs 1472726 n.881G>A non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.38
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.38
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.33
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.5
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 1.0
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 1.0
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 1.0
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.6
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.4
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.6
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.4
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.83
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.83
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 1.0
rrl 1476518 n.2861G>A non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 1.0
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 1.0
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 1.0
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 1.0
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 1.0
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 1.0
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
rpsA 1833979 c.438T>C synonymous_variant 1.0
rpsA 1834249 c.708T>C synonymous_variant 1.0
rpsA 1834261 c.720A>G synonymous_variant 1.0
rpsA 1834262 c.721_723delTCGinsAGC synonymous_variant 1.0
rpsA 1834303 c.762T>C synonymous_variant 1.0
rpsA 1834306 c.765T>C synonymous_variant 1.0
kasA 2518504 c.390T>C synonymous_variant 1.0
kasA 2518506 p.Ala131Glu missense_variant 1.0
kasA 2518519 c.405G>C synonymous_variant 1.0
kasA 2518528 c.414C>G synonymous_variant 1.0
kasA 2518540 c.426T>C synonymous_variant 1.0
kasA 2518561 c.447T>C synonymous_variant 1.0
kasA 2518567 c.453G>C synonymous_variant 1.0
kasA 2518570 c.456G>C synonymous_variant 1.0
kasA 2518573 c.459G>C synonymous_variant 1.0
kasA 2518574 p.Ile154Val missense_variant 1.0
kasA 2518579 c.465T>C synonymous_variant 1.0
kasA 2518588 c.474T>C synonymous_variant 1.0
kasA 2518591 c.477G>C synonymous_variant 1.0
kasA 2518609 p.Met165Ile missense_variant 1.0
kasA 2518624 c.510C>G synonymous_variant 1.0
thyX 3067391 c.555G>C synonymous_variant 1.0
thyX 3067394 c.552G>C synonymous_variant 1.0
thyX 3067439 c.507A>G synonymous_variant 1.0
thyX 3067445 c.501C>G synonymous_variant 1.0
thyX 3067457 c.489C>G synonymous_variant 1.0
thyX 3067462 c.484C>T synonymous_variant 1.0
thyX 3067465 p.Ile161Val missense_variant 1.0
thyX 3067466 c.480G>C synonymous_variant 1.0
thyX 3067475 c.471A>G synonymous_variant 1.0
thyX 3067490 p.Ala152Glu missense_variant 1.0
thyX 3067493 c.453A>G synonymous_variant 1.0
thyX 3067510 c.436C>T synonymous_variant 1.0
thyX 3067515 p.Ser144Thr missense_variant 1.0
rpoA 3877743 c.765T>C synonymous_variant 1.0
rpoA 3877764 c.744C>G synonymous_variant 1.0
rpoA 3877770 c.738A>G synonymous_variant 1.0
rpoA 3877776 c.732T>C synonymous_variant 1.0
rpoA 3877782 c.726T>C synonymous_variant 1.0
rpoA 3877791 c.717C>G synonymous_variant 1.0
rpoA 3877818 c.690A>G synonymous_variant 1.0
rpoA 3877839 c.669G>C synonymous_variant 1.0
rpoA 3877848 c.660C>T synonymous_variant 1.0
rpoA 3877857 c.651G>A synonymous_variant 1.0
rpoA 3877866 c.642G>C synonymous_variant 1.0
rpoA 3878094 c.414C>G synonymous_variant 1.0
rpoA 3878103 c.405A>G synonymous_variant 1.0
rpoA 3878106 c.402G>C synonymous_variant 1.0
rpoA 3878118 c.390T>C synonymous_variant 1.0
clpC1 4038356 c.2349T>C synonymous_variant 1.0
clpC1 4038359 c.2346A>G synonymous_variant 1.0
clpC1 4038368 c.2337T>C synonymous_variant 1.0
clpC1 4038419 c.2286T>C synonymous_variant 1.0
clpC1 4038433 c.2272C>T synonymous_variant 1.0
clpC1 4038434 c.2271G>A synonymous_variant 1.0
clpC1 4038444 p.Ala754Lys missense_variant 1.0
clpC1 4038446 c.2259T>C synonymous_variant 1.0
clpC1 4038456 p.Val750Glu missense_variant 1.0
clpC1 4038460 p.Leu749Met missense_variant 1.0
clpC1 4038486 p.Gly740Asn missense_variant 1.0
clpC1 4038489 p.Ala739Gly missense_variant 1.0
clpC1 4038494 c.2211G>C synonymous_variant 1.0
clpC1 4038497 p.Ser736Gln missense_variant 1.0
clpC1 4038509 c.2196C>T synonymous_variant 1.0
clpC1 4038530 p.Glu725Asp missense_variant 1.0
clpC1 4038596 c.2109A>G synonymous_variant 1.0
clpC1 4039454 c.1251A>G synonymous_variant 1.0
clpC1 4039463 c.1242C>G synonymous_variant 1.0
clpC1 4039466 c.1239T>C synonymous_variant 1.0
clpC1 4039469 c.1236T>C synonymous_variant 1.0
clpC1 4039481 c.1224T>C synonymous_variant 1.0
clpC1 4039484 c.1221T>C synonymous_variant 1.0
clpC1 4039517 c.1188C>G synonymous_variant 1.0
clpC1 4039556 c.1149G>C synonymous_variant 1.0
clpC1 4039559 c.1146C>G synonymous_variant 1.0
clpC1 4039562 c.1143C>G synonymous_variant 1.0
clpC1 4039565 c.1140G>C synonymous_variant 1.0
clpC1 4039570 p.Met379Leu missense_variant 1.0
clpC1 4039576 p.Ala377Pro missense_variant 1.0
clpC1 4039577 c.1128T>C synonymous_variant 1.0
clpC1 4039589 c.1116G>C synonymous_variant 1.0
clpC1 4039610 c.1095G>C synonymous_variant 1.0
clpC1 4039616 c.1089G>C synonymous_variant 1.0
clpC1 4039694 c.1011G>C synonymous_variant 1.0
clpC1 4039751 c.954A>G synonymous_variant 1.0
clpC1 4039757 c.948A>G synonymous_variant 1.0
clpC1 4039760 c.945T>C synonymous_variant 1.0
clpC1 4039766 c.939T>C synonymous_variant 1.0
clpC1 4039769 c.936C>G synonymous_variant 1.0
clpC1 4039775 c.930G>C synonymous_variant 1.0
clpC1 4039778 c.927A>G synonymous_variant 1.0
clpC1 4039781 c.924G>C synonymous_variant 1.0
clpC1 4039790 c.915C>G synonymous_variant 1.0
clpC1 4039817 c.888A>C synonymous_variant 1.0
clpC1 4039820 c.885T>G synonymous_variant 1.0
clpC1 4039826 c.879C>G synonymous_variant 1.0
clpC1 4039831 c.874T>C synonymous_variant 1.0
clpC1 4040369 c.336C>G synonymous_variant 1.0
clpC1 4040380 c.325T>C synonymous_variant 1.0
clpC1 4040381 c.324T>C synonymous_variant 1.0
clpC1 4040387 c.318A>G synonymous_variant 1.0
clpC1 4040393 c.312G>C synonymous_variant 1.0
clpC1 4040411 c.294T>C synonymous_variant 1.0
clpC1 4040418 p.Leu96Pro missense_variant 0.67
clpC1 4040423 c.282A>G synonymous_variant 1.0
clpC1 4040426 c.279T>C synonymous_variant 1.0
clpC1 4040431 c.274T>C synonymous_variant 1.0
clpC1 4040444 c.261C>T synonymous_variant 1.0
clpC1 4040450 c.255A>G synonymous_variant 1.0
clpC1 4040459 c.246C>G synonymous_variant 1.0
clpC1 4040465 c.240T>C synonymous_variant 1.0
clpC1 4040471 c.234T>C synonymous_variant 1.0
clpC1 4040477 c.228G>C synonymous_variant 1.0
clpC1 4040480 c.225T>G synonymous_variant 1.0
embB 4247951 p.Ser480Ala missense_variant 1.0
embB 4247956 c.1443G>C synonymous_variant 1.0
embB 4247974 c.1461C>G synonymous_variant 1.0