Line 148: |
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| | | |
| #This is a sample output of a peek command which summarizes the variants found in a VCF file. | | #This is a sample output of a peek command which summarizes the variants found in a VCF file. |
− | stats: no. of samples : 0
| + | stats: no. of samples : 0 |
− | no. of chromosomes : 22<br>
| + | no. of chromosomes : 25 <br> |
− | ========== Micro variants ==========<br>
| + | ========== Micro variants ========== <br> |
− | no. of SNPs : 77228885
| + | no. of SNP : 54247827 |
− | 2 alleles (ts/tv) : 77011302 (2.11) [52287790/24723512]
| + | 2 alleles : 53487808 (1.99) [35616038/17871770] (-nan) [0/0] |
− | 3 alleles (ts/tv) : 216560 (0.75) [185520/247600]
| + | 3 alleles : 389190 (0.60) [291224/487156] (-nan) [0/0] |
− | 4 alleles (ts/tv) : 1023 (0.50) [1023/2046]<br>
| + | 4 alleles : 370828 (0.50) [370828/741656] (-nan) [0/0] |
− | no. of MNPs : 0
| + | >=5 alleles : 1 (0.33) [1/3] (-nan) [0/0] <br> |
− | 2 alleles (ts/tv) : 0 (-nan) [0/0]
| + | no. of MNP : 122125 |
− | >=3 alleles (ts/tv) : 0 (-nan) [0/0]<br>
| + | 2 alleles : 121849 (1.56) [152383/97816] (-nan) [0/0] |
− | no. Indels : 2147564
| + | 3 alleles : 273 (0.89) [537/601] (-nan) [0/0] |
− | 2 alleles (ins/del) : 2124842 (0.47) [683250/1441592]
| + | 4 alleles : 3 (1.00) [9/9] (-nan) [0/0] <br> |
− | >=3 alleles (ins/del) : 22722 (2.12) [32411/15286]<br>
| + | no. of Indel : 6600770 |
− | no. SNP/MNP : 0
| + | 2 alleles : 6285861 (-nan) [0/0] (0.88) [2937096/3348765] |
− | 3 alleles (ts/tv) : 0 (-nan) [0/0]
| + | 3 alleles : 280892 (-nan) [0/0] (8.72) [503977/57807] |
− | >=4 alleles (ts/tv) : 0 (-nan) [0/0] <br>
| + | 4 alleles : 28245 (-nan) [0/0] (131.19) [84094/641] |
− | no. SNP/Indels : 12913
| + | >=5 alleles : 5772 (-nan) [0/0] (3847.00) [23082/6] <br> |
− | 2 alleles (ts/tv) (ins/del) : 412 (0.41) [120/292] (3.68) [324/88]
| + | no. of SNP/MNP : 1161 |
− | >=3 alleles (ts/tv) (ins/del) : 12501 (0.43) [7670/17649] (18.64) [12434/667]<br>
| + | 3 alleles : 1143 (1.57) [1565/994] (-nan) [0/0] |
− | no. MNP/Indels : 153
| + | 4 alleles : 15 (1.36) [34/25] (-nan) [0/0] |
− | 2 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
| + | >=5 alleles : 3 (0.67) [8/12] (-nan) [0/0] <br> |
− | >=3 alleles (ts/tv) (ins/del) : 153 (0.30) [138/465] (0.27) [67/248]<br>
| + | no. of SNP/Indel : 115153 |
− | no. SNP/MNP/Indels : 2
| + | 2 alleles : 42717 (0.65) [16778/25939] (0.57) [15441/27276] |
− | 3 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]
| + | 3 alleles : 66401 (0.72) [29681/41397] (0.33) [31458/96168] |
− | 4 alleles (ts/tv) (ins/del) : 2 (0.00) [3/5] (1.00) [3/3] | + | 4 alleles : 4631 (0.55) [2420/4386] (0.25) [2602/10306] |
− | >=5 alleles (ts/tv) (ins/del) : 0 (-nan) [0/0] (-nan) [0/0]<br>
| + | >=5 alleles : 1404 (0.62) [1197/1926] (0.10) [513/4989] <br> |
− | no. of clumped variants : 19025
| + | no. of MNP/Indel : 15619 |
− | 2 alleles : 0 (-nan) [0/0] (-nan) [0/0]
| + | 2 alleles : 12820 (0.51) [12099/23648] (0.77) [5594/7226] |
− | 3 alleles : 18508 (0.16) [12152/75366] (0.00) [93/18653] | + | 3 alleles : 2455 (0.40) [1796/4469] (0.45) [1144/2546] |
− | 4 alleles : 451 (0.15) [369/2390] (0.33) [201/609]
| + | 4 alleles : 292 (0.24) [215/891] (1.42) [415/292] |
− | >=5 alleles : 66 (0.09) [37/414] (1.19) [107/90]<br>
| + | >=5 alleles : 52 (0.43) [96/225] (2.47) [126/51] <br> |
− | ====== Other useful categories =====<br>
| + | no. of SNP/MNP/Indel : 273 |
− | no. complex variants : 32093
| + | 3 alleles : 167 (0.63) [201/321] (0.38) [70/184] |
− | 2 alleles (ts/tv) (ins/del) : 412 (0.41) [120/292] (3.68) [324/88]
| + | 4 alleles : 85 (0.35) [71/203] (0.28) [31/111] |
− | >=3 alleles (ts/tv) (ins/del) : 31681 (0.21) [20369/96289] (0.64) [12905/20270]<br>
| + | >=5 alleles : 21 (0.35) [24/68] (0.68) [25/37]<br> |
| + | no. of Clumped : 0 <br> |
| + | no. of SNP/Clumped : 0 <br> |
| + | no. of MNP/Clumped : 61175 |
| + | 2 alleles : 60617 (1.68) [84410/50220] (-nan) [0/0] |
| + | 3 alleles : 549 (1.23) [1777/1449] (-nan) [0/0] |
| + | 4 alleles : 8 (1.43) [53/37] (-nan) [0/0] |
| + | >=5 alleles : 1 (1.00) [5/5] (-nan) [0/0] <br> |
| + | no. of SNP/MNP/Clumped : 290 |
| + | 3 alleles : 282 (1.35) [665/494] (-nan) [0/0] |
| + | 4 alleles : 8 (0.57) [13/23] (-nan) [0/0] <br> |
| + | no. of Indel/Clumped : 27638 |
| + | 2 alleles : 25971 (0.65) [31435/48526] (0.79) [11444/14527] |
| + | 3 alleles : 1585 (0.74) [3568/4793] (0.87) [1383/1582] |
| + | 4 alleles : 70 (0.55) [96/175] (1.61) [124/77] |
| + | >=5 alleles : 12 (0.59) [37/63] (4.71) [33/7] <br> |
| + | no. of SNP/Indel/Clumped : 456 |
| + | 3 alleles : 257 (0.84) [332/394] (0.33) [111/340] |
| + | 4 alleles : 174 (0.38) [105/279] (0.58) [186/321] |
| + | >=5 alleles : 25 (0.19) [12/63] (0.94) [44/47] <br> |
| + | no. of MNP/Indel/Clumped : 153 |
| + | 3 alleles : 138 (0.50) [233/466] (0.84) [102/122] |
| + | 4 alleles : 12 (0.35) [14/40] (1.42) [17/12] |
| + | >=5 alleles : 3 (0.64) [7/11] (0.67) [4/6] <br> |
| + | no. of SNP/MNP/Indel/Clumped : 6 |
| + | 4 alleles : 1 (3.00) [3/1] (0.00) [0/3] |
| + | >=5 alleles : 5 (0.62) [8/13] (2.00) [12/6] <br> |
| + | no. of Reference : 0 <br> |
| + | ====== Other useful categories ===== <br> |
| + | no. of Block Substitutions : 184751 |
| + | 2 alleles : 182466 (1.60) [236793/148036] (-nan) [0/0] |
| + | 3 alleles : 2247 (1.28) [4544/3538] (-nan) [0/0] |
| + | 4 alleles : 34 (1.16) [109/94] (-nan) [0/0] |
| + | >=5 alleles : 4 (0.76) [13/17] (-nan) [0/0] <br> |
| + | no. of Complex Substitutions : 159298 |
| + | 2 alleles : 81508 (0.61) [60312/98113] (0.66) [32479/49029] |
| + | 3 alleles : 71003 (0.69) [35811/51840] (0.34) [34268/100942] |
| + | 4 alleles : 5265 (0.49) [2924/5975] (0.30) [3375/11122] |
| + | >=5 alleles : 1522 (0.58) [1381/2369] (0.15) [757/5143] <br> |
| ======= Structural variants ========<br> | | ======= Structural variants ========<br> |
| no. of structural variants : 41217 | | no. of structural variants : 41217 |