BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081966.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 = 3,040,203 number of mapped reads = 2,778,072 (91.38%) number of supplementary alignments = 17,998 (0.59%) number of secondary alignments = 0 number of mapped bases = 190,984,415 bp number of sequenced bases = 190,902,692 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,126 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.635 >>>>>>> ACTG content number of A's = 54,994,568 bp (28.81%) number of C's = 35,417,242 bp (18.55%) number of T's = 59,786,350 bp (31.32%) number of G's = 40,680,193 bp (21.31%) number of N's = 24,339 bp (0.01%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,535,785 number of insertions = 14,334 mapped reads with insertion percentage = 0.51% number of deletions = 47,008 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.0617X std coverageData = 0.5941X There is a 5.28% of reference with a coverageData >= 1X There is a 0.63% 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 17229050 0.06912339849295701 1.1368334919903713 chr2 243199373 16427415 0.06754711082252667 0.7535197232333011 chr3 198022430 12152205 0.06136782080696616 0.2784755464176894 chr4 191154276 9891042 0.051743765334341774 0.2751931934801063 chr5 180915260 9692071 0.0535724349620922 0.2632350316218143 chr6 171115067 16829200 0.09835019379094186 0.47655171005807656 chr7 159138663 12330034 0.07747981394062611 0.8378784043627977 chr8 146364022 10904124 0.07450002979557367 0.9223995777179722 chr9 141213431 9392662 0.06651394228924301 0.5901547315596452 chr10 135534747 7822717 0.05771742798914879 0.6000229003855484 chr11 135006516 8599496 0.06369689593352665 0.39609527470588485 chr12 133851895 8356933 0.06243417771560126 0.29734652519421495 chr13 115169878 5154533 0.04475591265278583 0.2358296873639629 chr14 107349540 4894534 0.04559436398143858 0.28649525279264315 chr15 102531392 4276468 0.041708865124936566 0.22916757911805355 chr16 90354753 4159074 0.04603049493146199 0.3055293956810766 chr17 81195210 4909291 0.0604628154788934 0.31083722307045314 chr18 78077248 5430778 0.0695564730970026 0.9964895084196463 chr19 59128983 4088331 0.06914258951485772 0.7930176537692635 chr20 63025520 4667293 0.0740540181183749 0.31372247553363325 chr21 48129895 1987776 0.04130023553967861 0.2684448908422632 chr22 51304566 1502001 0.029276166179828908 0.18842700393118442 chrMT 16571 72785 4.392311870134573 2.9673589696909843 chrX 155270560 9809107 0.0631742875146454 0.34213100654990525 chrY 59373566 405495 0.006829554418206917 0.15936563520775066