MultiQC Analysis of 2016-07-01 MiSeq mcf-trimmed data


MultiQC: a new program which summarises and contracts all the FastQC reports (given below)

FastQC Analysis of 2016-07-01 MiSeq mcf-trimmed data

500005_R1_tr_ | 500005_R2_tr_
500024_R1_tr_ | 500024_R2_tr_
500519_R1_tr_ | 500519_R2_tr_
500523_R1_tr_ | 500523_R2_tr_
501725_R1_tr_ | 501725_R2_tr_
502749_R1_tr_ | 502749_R2_tr_
502836_R1_tr_ | 502836_R2_tr_
503710_R1_tr_ | 503710_R2_tr_
504302_R1_tr_ | 504302_R2_tr_
504782_R1_tr_ | 504782_R2_tr_
505137_R1_tr_ | 505137_R2_tr_
505907_R1_tr_ | 505907_R2_tr_
506683_R1_tr_ | 506683_R2_tr_
506776_R1_tr_ | 506776_R2_tr_
606111_R1_tr_ | 606111_R2_tr_
607239_R1_tr_ | 607239_R2_tr_
BS20102N_R1_tr_ | BS20102N_R2_tr_
MU572163T_R1_tr_ | MU572163T_R2_tr_
Undetermined_R1_tr_ | Undetermined_R2_tr_

SPAdes assembly statistics

filename total_length number mean_length longest shortest N_count Gaps N50 N50n N70 N70n N90 N90n
500005_mcftrimassembly/scaffolds.fasta 4,322,959 832 5195.86 61,991 61 241 3 14,248 94 9,235 171 3,399 316
500519_mcftrimassembly/scaffolds.fasta 4,362,950 863 5055.56 63,039 70 471 4 16,163 84 9,884 154 3,968 287
500523_mcftrimassembly/scaffolds.fasta 5,406,709 2,975 1817.38 75,480 49 130 13 16,658 98 6,248 196 423 1,453
501725_mcftrimassembly/scaffolds.fasta 4,984,680 491 10152.10 133,815 55 516 12 37,354 41 22,097 76 9,299 142
502749_mcftrimassembly/scaffolds.fasta 4,716,162 1,666 2830.83 81,973 48 80 8 17,599 80 9,616 151 743 416
502836_mcftrimassembly/scaffolds.fasta 4,539,314 1,115 4071.13 88,852 59 173 17 22,927 63 13,784 113 3,119 242
503710_mcftrimassembly/scaffolds.fasta 4,382,356 1,298 3376.24 37,141 33 139 14 9,363 136 5,747 256 1,937 500
504302_mcftrimassembly/scaffolds.fasta 8,018,195 7,705 1040.65 66,289 78 95 10 3,692 264 612 1,945 385 5,372
504782_mcftrimassembly/scaffolds.fasta 5,478,137 2,968 1845.73 82,578 43 662 20 14,586 102 5,256 221 444 1,419
505137_mcftrimassembly/scaffolds.fasta 8,887,183 8,243 1078.15 117,022 78 590 59 1,402 1,743 902 3,333 488 5,974
505907_mcftrimassembly/scaffolds.fasta 11,062,707 6,522 1696.21 44,535 3 1,163 43 5,788 552 3,502 1,044 1,079 2,090
506683_mcftrimassembly/scaffolds.fasta 4,309,935 1,143 3770.72 44,443 60 786 28 9,320 143 5,448 262 2,074 504
506776_mcftrimassembly/scaffolds.fasta 4,372,789 587 7449.39 90,336 71 110 11 26,579 54 15,872 96 6,875 177
606111_mcftrimassembly/scaffolds.fasta 4,472,723 1,612 2774.64 65,766 78 60 6 9,014 150 4,906 282 1,229 618
607239_mcftrimassembly/scaffolds.fasta 4,374,179 705 6204.51 103,954 78 10 1 20,821 65 13,205 116 4,865 221
BS20102N_mcftrimassembly/scaffolds.fasta 1,848,135 102 18118.97 336,444 78 0 0 209,922 4 115,362 6 67,076 10
MU572163T_mcftrimassembly/scaffolds.fasta 2,962,496 500 5924.99 125,565 78 256 2 22,522 38 14,108 72 4,073 140
Undetermined_mcftrimassembly/scaffolds.fasta 4,122,476 7,112 579.65 6,645 5 40 4 646 1,907 441 3,477 352 5,570