BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231796.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 = 5,630,342 number of mapped reads = 5,118,568 (90.91%) number of supplementary alignments = 29,597 (0.53%) number of secondary alignments = 0 number of mapped bases = 320,746,457 bp number of sequenced bases = 320,604,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 713,802 duplication rate = 11.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7019 >>>>>>> ACTG content number of A's = 79,321,813 bp (24.74%) number of C's = 57,174,732 bp (17.83%) number of T's = 105,975,580 bp (33.05%) number of G's = 78,014,395 bp (24.33%) number of N's = 118,094 bp (0.04%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,273,998 number of insertions = 23,101 mapped reads with insertion percentage = 0.45% number of deletions = 85,156 mapped reads with deletion percentage = 1.65% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.1036X std coverageData = 1.1942X There is a 7.11% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% 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 52429400 0.21034812186084784 2.095481951604179 chr2 243199373 27706103 0.11392341459696115 2.2257153707595516 chr3 198022430 22000408 0.11110058592857384 0.48951489434907647 chr4 191154276 3222620 0.016858738749846225 0.3017893691505919 chr5 180915260 27709924 0.15316521116018628 0.5378650126231633 chr6 171115067 10152732 0.05933277634750889 0.7149768372409784 chr7 159138663 36860016 0.23162200376158745 2.3950340985152643 chr8 146364022 8057782 0.05505302389134947 0.6488975485265872 chr9 141213431 8275022 0.05859939767344085 0.619075665531123 chr10 135534747 14349945 0.10587650265064501 1.1784236514498252 chr11 135006516 14906582 0.11041379662000907 0.7423542642867448 chr12 133851895 6886341 0.05144746736682361 0.3235572488899776 chr13 115169878 5702983 0.04951800851955405 0.4582630372638052 chr14 107349540 14452664 0.13463182049965003 0.5192119431607928 chr15 102531392 6871223 0.06701579746425368 0.4480041597122468 chr16 90354753 11419777 0.12638822663817142 0.5966731304458964 chr17 81195210 5712936 0.07036050525640614 0.4077894426683244 chr18 78077248 7454007 0.0954696430898794 1.836468634797988 chr19 59128983 6983328 0.11810329969652954 1.4015038423353403 chr20 63025520 10154258 0.16111343468487052 0.5632505992054658 chr21 48129895 8530213 0.17723315207731077 0.6277238488075253 chr22 51304566 2797400 0.05452536134892945 0.3132506200421297 chrMT 16571 340089 20.52314283990103 20.334020014059337 chrX 155270560 6971687 0.04490025024705263 0.4309744618757628 chrY 59373566 799017 0.013457453439801814 0.3883817765750377