BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082501.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 = 2,683,751 number of mapped reads = 2,443,145 (91.03%) number of supplementary alignments = 21,446 (0.8%) number of secondary alignments = 0 number of mapped bases = 166,393,432 bp number of sequenced bases = 166,322,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,461 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2743 >>>>>>> ACTG content number of A's = 47,312,637 bp (28.45%) number of C's = 31,090,220 bp (18.69%) number of T's = 52,227,400 bp (31.4%) number of G's = 35,689,112 bp (21.46%) number of N's = 3,562 bp (0%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,413,207 number of insertions = 13,436 mapped reads with insertion percentage = 0.55% number of deletions = 43,657 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.4757X There is a 4.57% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 12692977 0.050924555168911693 0.7782543562024451 chr2 243199373 14327657 0.05891321520800138 0.5568716898428365 chr3 198022430 10866475 0.054874970476829314 0.2648938162954609 chr4 191154276 11069375 0.05790806897775073 0.2878651577645529 chr5 180915260 9830803 0.05433926911416981 0.26546576848670145 chr6 171115067 10029479 0.058612483259583445 0.36523147008567763 chr7 159138663 9129245 0.05736660612763851 0.4374653133540549 chr8 146364022 8940593 0.06108463594967348 0.9653047641130117 chr9 141213431 7198372 0.05097512289748133 0.4358077398428269 chr10 135534747 7853555 0.05794495635868196 0.40080543374378 chr11 135006516 7789992 0.057700859416296615 0.5146987976868186 chr12 133851895 7699480 0.05752238322811941 0.2808967177651654 chr13 115169878 5192844 0.04508856039597437 0.24107190548701266 chr14 107349540 5088899 0.047404944632273224 0.27002547824422746 chr15 102531392 4867894 0.047477108279189266 0.25788654900891533 chr16 90354753 4458556 0.049345007893497314 0.2792308600762835 chr17 81195210 4288560 0.05281789406049938 0.3346921476446164 chr18 78077248 4731545 0.06060081677059109 0.8945906028989817 chr19 59128983 2896932 0.048993435249850316 0.5380261633466643 chr20 63025520 3274079 0.05194846468541632 0.2711688476559492 chr21 48129895 2235883 0.04645518133791898 0.2646254475237628 chr22 51304566 1756450 0.03423574424155542 0.20771636566795232 chrMT 16571 9578 0.5779977068372458 0.9139792292826071 chrX 155270560 9790524 0.06305460610176199 0.34517903456316545 chrY 59373566 373685 0.006293794110328492 0.13784899165540093