BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714180.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 = 1,742,602 number of mapped reads = 1,631,107 (93.6%) number of supplementary alignments = 85,505 (4.91%) number of secondary alignments = 0 number of mapped bases = 207,261,124 bp number of sequenced bases = 203,411,448 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,537,999 duplication rate = 47.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4749 >>>>>>> ACTG content number of A's = 59,642,816 bp (29.32%) number of C's = 41,673,245 bp (20.49%) number of T's = 56,415,520 bp (27.73%) number of G's = 45,678,422 bp (22.46%) number of N's = 1,445 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0363 number of mismatches = 6,944,433 number of insertions = 173,042 mapped reads with insertion percentage = 10.28% number of deletions = 623,813 mapped reads with deletion percentage = 36.62% homopolymer indels = 27.67% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 11.0673X There is a 0.1% of reference with a coverageData >= 1X There is a 0.07% 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 0.03% of reference with a coverageData >= 9X There is a 0.03% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 13141132 0.052722564731343236 8.056200191900963 chr2 243199373 21592874 0.08878671739009787 17.639807549992376 chr3 198022430 10662813 0.053846491026294345 5.991078251313664 chr4 191154276 13444558 0.0703335456644454 10.304190684853095 chr5 180915260 12920811 0.07141913291338718 13.716375191440102 chr6 171115067 11756409 0.06870469799132299 9.602944220085545 chr7 159138663 9608564 0.06037856432160675 10.269014051863232 chr8 146364022 7552446 0.05160042677701218 5.973074104906198 chr9 141213431 7974538 0.05647152642300717 8.216591186285848 chr10 135534747 10421320 0.07689039328047736 15.221567071856743 chr11 135006516 8520996 0.06311544251686341 10.46022807035617 chr12 133851895 8288649 0.06192403178154482 7.351733162999574 chr13 115169878 6884365 0.05977574275106899 9.718745377701293 chr14 107349540 5379999 0.05011664698330333 11.098853788045663 chr15 102531392 4496799 0.04385777772333375 5.640944998558938 chr16 90354753 2464756 0.027278653509240403 3.11662614163693 chr17 81195210 2312183 0.028476839951519308 4.624130885751599 chr18 78077248 5377144 0.06886953802470087 10.98669418492975 chr19 59128983 917079 0.015509805064633024 1.736250017471462 chr20 63025520 3423280 0.05431577557789289 8.766725880170181 chr21 48129895 1715345 0.035639907379810404 5.0274587942528495 chr22 51304566 1218271 0.02374585918921914 4.03867656572606 chrMT 16571 8130 0.49061613662422304 3.908963751341984 chrX 155270560 35076622 0.22590645644608998 21.954030665053047 chrY 59373566 2102041 0.03540365084354206 8.038369476776806