BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818755.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,832,032 number of mapped reads = 1,784,476 (97.4%) number of supplementary alignments = 14,575 (0.8%) number of secondary alignments = 0 number of mapped bases = 121,209,496 bp number of sequenced bases = 121,160,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 875,491 duplication rate = 42.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7852 >>>>>>> ACTG content number of A's = 33,082,824 bp (27.3%) number of C's = 27,596,427 bp (22.78%) number of T's = 35,282,263 bp (29.12%) number of G's = 25,191,242 bp (20.79%) number of N's = 7,653 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 606,002 number of insertions = 14,397 mapped reads with insertion percentage = 0.8% number of deletions = 30,941 mapped reads with deletion percentage = 1.71% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0392X std coverageData = 0.4696X There is a 1.69% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 10189453 0.04088035150773005 0.6621170533754547 chr2 243199373 10705012 0.04401743256139069 0.6296579196246889 chr3 198022430 8227368 0.04154765700027012 0.3925713101863909 chr4 191154276 7564220 0.039571283249766276 0.40800242689376737 chr5 180915260 7393203 0.040865557720227694 0.4012071218310128 chr6 171115067 7357851 0.04299943382542696 0.42177698165324684 chr7 159138663 6558103 0.04120999181701055 0.4322227490495174 chr8 146364022 6098640 0.04166761692296212 0.43681337369347195 chr9 141213431 5203794 0.03685055991593321 0.4152066502425335 chr10 135534747 5817525 0.042922756922252565 0.4828740436817211 chr11 135006516 5581550 0.04134281933473492 0.42606792976440455 chr12 133851895 5589113 0.04175594973832832 0.4060404479494835 chr13 115169878 3790024 0.03290811856204276 0.34716477984443833 chr14 107349540 3797474 0.03537485116377769 0.38848790144560724 chr15 102531392 3644545 0.035545650253143934 0.36611076085351685 chr16 90354753 3770689 0.04173204922601028 0.5034292163924582 chr17 81195210 3552043 0.04374695256037887 0.4231698568395448 chr18 78077248 3175931 0.040676779488949204 0.5395251254561193 chr19 59128983 2538609 0.04293341219821082 0.5712728370349094 chr20 63025520 2601069 0.04127009186120162 0.4113432304634958 chr21 48129895 1536904 0.031932419549221956 0.3578250333176986 chr22 51304566 1569169 0.030585367392056292 0.3592890515025145 chrMT 16571 297761 17.968800917265103 16.149711770143224 chrX 155270560 3629506 0.023375364911416563 0.3084282425430546 chrY 59373566 1019940 0.01717835172642317 0.630717381167389