BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714176.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,623,584 number of mapped reads = 1,306,044 (80.44%) number of supplementary alignments = 42,582 (2.62%) number of secondary alignments = 0 number of mapped bases = 168,776,077 bp number of sequenced bases = 164,906,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,166,018 duplication rate = 45.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.56 >>>>>>> ACTG content number of A's = 44,970,987 bp (27.27%) number of C's = 36,538,197 bp (22.16%) number of T's = 42,733,654 bp (25.91%) number of G's = 40,662,253 bp (24.66%) number of N's = 1,124 bp (0%) GC percentage = 46.81% >>>>>>> Mismatches and indels general error rate = 0.0447 number of mismatches = 6,862,114 number of insertions = 180,152 mapped reads with insertion percentage = 13.39% number of deletions = 630,391 mapped reads with deletion percentage = 45.89% homopolymer indels = 28.96% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 6.3908X There is a 0.1% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 16436198 0.06594245556563728 8.011748739994443 chr2 243199373 15527255 0.06384578549057361 11.464194457053111 chr3 198022430 8436189 0.04260218905504796 4.1459884534861 chr4 191154276 7582774 0.03966834621057601 4.484291421164327 chr5 180915260 8702951 0.048105123912709186 4.702485701927184 chr6 171115067 6786348 0.03965955844203947 3.80847092086803 chr7 159138663 6682258 0.04199016049292811 4.425581005820093 chr8 146364022 7686946 0.05251936845517951 6.443161876779349 chr9 141213431 5817504 0.04119653462707807 4.468597429014953 chr10 135534747 9174816 0.06769346018700283 5.9945479987137205 chr11 135006516 7931169 0.058746564499153504 6.4958954722383595 chr12 133851895 7111976 0.053133173796306735 6.491179691586431 chr13 115169878 4148343 0.03601934005695482 4.487803805034142 chr14 107349540 6159215 0.057375327365166165 6.333441181481463 chr15 102531392 5438678 0.05304402772567449 4.816784726881408 chr16 90354753 6082583 0.06731890462917872 6.382623155602442 chr17 81195210 7364789 0.09070472260617345 9.030016495077861 chr18 78077248 3816496 0.048881026134527696 4.4005224641058565 chr19 59128983 4607130 0.07791661155410029 7.983556786133736 chr20 63025520 5370662 0.08521408470727414 8.26273164587763 chr21 48129895 1534741 0.03188747866580636 3.153191526666321 chr22 51304566 2610578 0.05088393107155414 5.756758415572644 chrMT 16571 258193 15.581015026250679 142.43502424430295 chrX 155270560 13084176 0.08426694667682012 5.70257977498794 chrY 59373566 424109 0.007143060937252784 1.0336434433646728