BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089597.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 23,268,481 number of mapped reads = 18,828,749 (80.92%) number of supplementary alignments = 634 (0%) number of secondary alignments = 0 number of mapped bases = 876,331,615 bp number of sequenced bases = 876,163,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,029,085 duplication rate = 8.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4465 >>>>>>> ACTG content number of A's = 269,593,184 bp (30.77%) number of C's = 181,176,415 bp (20.68%) number of T's = 234,977,200 bp (26.82%) number of G's = 189,763,858 bp (21.66%) number of N's = 652,607 bp (0.07%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 4,716,534 number of insertions = 36,685 mapped reads with insertion percentage = 0.19% number of deletions = 113,171 mapped reads with deletion percentage = 0.6% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.2831X std coverageData = 1.4495X There is a 14.7% of reference with a coverageData >= 1X There is a 6.04% of reference with a coverageData >= 2X There is a 2.92% of reference with a coverageData >= 3X There is a 1.57% of reference with a coverageData >= 4X There is a 0.91% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% 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 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 70006653 0.2808685198822433 2.0595793670590408 chr2 243199373 72326902 0.29739756771494635 1.7406334406034427 chr3 198022430 59188806 0.2988995034552399 0.9767367870546533 chr4 191154276 56799037 0.29713715114591527 1.0736845450064714 chr5 180915260 51897654 0.28686167214418506 0.9598767855750506 chr6 171115067 51486455 0.30088791070630855 1.176430501642524 chr7 159138663 48019245 0.3017446803609252 1.9533493209987656 chr8 146364022 44412263 0.30343702224854135 2.201596750039562 chr9 141213431 36415129 0.2578729851836827 1.3778235473043101 chr10 135534747 41095820 0.30321243009366444 1.5181611994609363 chr11 135006516 40422747 0.2994133038734219 1.413288622834477 chr12 133851895 40116019 0.29970452790377006 1.0347226100343996 chr13 115169878 28167874 0.2445767460133977 0.8875862165744061 chr14 107349540 27259601 0.2539330955679922 1.103791996271167 chr15 102531392 25112370 0.24492372053234193 0.8874117104923407 chr16 90354753 24953825 0.27617611881469034 1.075920800615262 chr17 81195210 23513529 0.2895925634036786 1.1431808495550349 chr18 78077248 22633025 0.2898799020170383 2.1631688737898567 chr19 59128983 17396194 0.29420756315054497 1.9473529468379018 chr20 63025520 18631078 0.2956116506456432 1.0563700195931631 chr21 48129895 11554052 0.2400597798935568 1.1112401041725657 chr22 51304566 10111164 0.19708117207345638 0.7979402602059169 chrMT 16571 404368 24.402148331422364 20.14641753084885 chrX 155270560 51839521 0.3338657437701004 1.3229297042338084 chrY 59373566 2568284 0.04325635418293723 0.6952078266204144