BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237581.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,312,683 number of mapped reads = 1,882,020 (81.38%) number of supplementary alignments = 10,248 (0.44%) number of secondary alignments = 0 number of mapped bases = 118,651,618 bp number of sequenced bases = 118,580,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,042 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8682 >>>>>>> ACTG content number of A's = 29,762,832 bp (25.1%) number of C's = 22,410,619 bp (18.9%) number of T's = 36,029,895 bp (30.38%) number of G's = 30,350,706 bp (25.59%) number of N's = 26,719 bp (0.02%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,120,998 number of insertions = 11,300 mapped reads with insertion percentage = 0.59% number of deletions = 42,270 mapped reads with deletion percentage = 2.22% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3785X There is a 2.92% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10359377 0.04156209103286447 0.4829307350026527 chr2 243199373 10015015 0.04118026652971675 0.5360048564354155 chr3 198022430 7987791 0.040337809206765114 0.2874680312772519 chr4 191154276 7463117 0.039042375384791286 0.29968456068776633 chr5 180915260 6473692 0.0357830069171611 0.2574085418397044 chr6 171115067 6342394 0.037065082059664564 0.29525244812420687 chr7 159138663 7100425 0.044617850031830414 0.5635734426122548 chr8 146364022 6167060 0.042135081529803824 0.3531151156262412 chr9 141213431 4787290 0.033901095427672175 0.40544609447282487 chr10 135534747 5134374 0.03788234466546059 0.37099479914221284 chr11 135006516 4998429 0.03702361299361284 0.421417270152632 chr12 133851895 6907703 0.05160706167066219 0.34217126861304076 chr13 115169878 3825095 0.033212633949304 0.2616503878114786 chr14 107349540 3338423 0.031098624176684873 0.290759315135468 chr15 102531392 3727228 0.03635206669192592 0.28454050370337236 chr16 90354753 3355477 0.03713669606290662 0.3130481966026194 chr17 81195210 3090382 0.0380611368577038 0.30849450081615404 chr18 78077248 3015237 0.038618638300366326 0.5597779428709196 chr19 59128983 2560489 0.04330345069523689 0.3929463824630831 chr20 63025520 2505123 0.039747756147033776 0.2942231311632092 chr21 48129895 1426407 0.029636611507255523 0.27479343531774764 chr22 51304566 1375046 0.026801630092728977 0.23538764608615317 chrMT 16571 107836 6.5075131253394485 5.458000310173099 chrX 155270560 6143529 0.03956660554325302 0.3017771168084815 chrY 59373566 444679 0.007489511409841882 0.18149864301454105