BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234111.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,900,017 number of mapped reads = 3,608,383 (92.52%) number of supplementary alignments = 37,734 (0.97%) number of secondary alignments = 0 number of mapped bases = 248,665,698 bp number of sequenced bases = 248,578,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 755,218 duplication rate = 9.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9906 >>>>>>> ACTG content number of A's = 62,685,370 bp (25.22%) number of C's = 44,160,461 bp (17.77%) number of T's = 68,146,373 bp (27.41%) number of G's = 73,533,578 bp (29.58%) number of N's = 53,061 bp (0.02%) GC percentage = 47.35% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,551,658 number of insertions = 16,054 mapped reads with insertion percentage = 0.44% number of deletions = 52,719 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.0803X std coverageData = 47.4348X There is a 2.86% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 12164694 0.048805069978140596 0.5249585142810499 chr2 243199373 34842882 0.14326879864118727 169.220161979131 chr3 198022430 34532018 0.17438437655774652 0.881436905591076 chr4 191154276 8944854 0.046793899603899 0.4835568195150051 chr5 180915260 2848785 0.015746515799717503 0.24926999682053333 chr6 171115067 8114661 0.047422247159567776 0.4953629141018178 chr7 159138663 24660867 0.1549646486598923 1.032214408552376 chr8 146364022 5353203 0.036574582515913646 0.667411482865337 chr9 141213431 8025325 0.056831173516349164 0.6264244279404866 chr10 135534747 7376982 0.054428714136309266 0.6429478757312493 chr11 135006516 16468374 0.1219820678877455 0.8906224158492255 chr12 133851895 19918257 0.1488081808628858 0.8283291621886004 chr13 115169878 19926960 0.17302232446577742 0.8850500362172344 chr14 107349540 2913377 0.027139166129635954 0.48872880816023045 chr15 102531392 6639331 0.06475412915490311 0.5415428553816285 chr16 90354753 3436086 0.03802883507412167 0.4958055008524799 chr17 81195210 7860520 0.09681014434225861 0.6624217542549614 chr18 78077248 6867714 0.08796050291116818 1.5961895479031833 chr19 59128983 1691476 0.02860654647146561 0.38170082991178067 chr20 63025520 1766864 0.028034104280297886 0.37667401466442774 chr21 48129895 5903649 0.12266074962349284 0.7843820524543014 chr22 51304566 5220695 0.10175887658809939 0.6692919004773645 chrMT 16571 15784 0.9525073924325629 1.8668804993748958 chrX 155270560 2681747 0.01727144540471806 0.36001880313144535 chrY 59373566 490593 0.008262818507481933 0.19423240329516878