BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081240.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,209,003 number of mapped reads = 1,953,042 (88.41%) number of supplementary alignments = 21,117 (0.96%) number of secondary alignments = 0 number of mapped bases = 123,245,097 bp number of sequenced bases = 123,200,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,555 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2299 >>>>>>> ACTG content number of A's = 36,623,291 bp (29.73%) number of C's = 23,978,129 bp (19.46%) number of T's = 37,176,581 bp (30.18%) number of G's = 25,414,360 bp (20.63%) number of N's = 8,284 bp (0.01%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,099,792 number of insertions = 9,362 mapped reads with insertion percentage = 0.48% number of deletions = 27,622 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.2917X There is a 3.3% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 11930970 0.047867363187030935 0.3824297687804519 chr2 243199373 9327513 0.038353359570544615 0.3117576911394972 chr3 198022430 8983900 0.04536809289735511 0.2517226067278486 chr4 191154276 7066974 0.03697000217771744 0.23077774686552685 chr5 180915260 7005281 0.03872133837687324 0.23037746633743375 chr6 171115067 8893997 0.05197670290483537 0.3007621258303577 chr7 159138663 8620489 0.05416967088632635 0.4368130433218094 chr8 146364022 6949875 0.047483492903741056 0.41598568777267386 chr9 141213431 3063053 0.021690946663564883 0.1964570421000269 chr10 135534747 3286509 0.024248460802453853 0.2799777100746492 chr11 135006516 7038103 0.05213158007869783 0.34209046517199493 chr12 133851895 3377851 0.025235735362581158 0.1877511711038187 chr13 115169878 4330102 0.03759752181034697 0.22954313274406238 chr14 107349540 4046385 0.03769354763886273 0.23377092871774663 chr15 102531392 3734451 0.03642251340935662 0.23905925810024156 chr16 90354753 3315508 0.036694339698986285 0.2316625740908311 chr17 81195210 1674297 0.020620637596725225 0.18864523023371096 chr18 78077248 3163937 0.04052316239424832 0.3117364496485437 chr19 59128983 2923064 0.04943538433596938 0.3239695347621819 chr20 63025520 2304899 0.03657088430210492 0.22496306364799265 chr21 48129895 1750563 0.03637163555000483 0.22952031808191392 chr22 51304566 794926 0.015494254449009471 0.14249186421396526 chrMT 16571 131399 7.929455072113934 6.222210062691117 chrX 155270560 9172593 0.05907490125623299 0.30287488543669533 chrY 59373566 358458 0.00603733317954997 0.11154121681586729