BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234037.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 = 1,435,542 number of mapped reads = 1,009,282 (70.31%) number of supplementary alignments = 8,315 (0.58%) number of secondary alignments = 0 number of mapped bases = 66,657,582 bp number of sequenced bases = 66,614,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,329 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3975 >>>>>>> ACTG content number of A's = 18,992,659 bp (28.51%) number of C's = 11,772,655 bp (17.67%) number of T's = 21,761,467 bp (32.67%) number of G's = 14,075,508 bp (21.13%) number of N's = 11,957 bp (0.02%) GC percentage = 38.8% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 547,923 number of insertions = 5,210 mapped reads with insertion percentage = 0.51% number of deletions = 24,757 mapped reads with deletion percentage = 2.41% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2216X There is a 1.77% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4918959 0.019734991954142415 0.2929473432349288 chr2 243199373 5502668 0.02262616030675375 0.2393173318107087 chr3 198022430 5857820 0.029581598407816732 0.20296180777134407 chr4 191154276 4275076 0.022364532405228538 0.17880540702371606 chr5 180915260 5788199 0.031993978838490464 0.21172403031187503 chr6 171115067 3994520 0.023344057715268287 0.19758070483423895 chr7 159138663 3078574 0.01934522976355532 0.20241960936211054 chr8 146364022 3162280 0.021605582825538917 0.4098823984473055 chr9 141213431 2298826 0.016279088920373302 0.18861768564427103 chr10 135534747 2513266 0.01854333339331795 0.19908399745419733 chr11 135006516 2528678 0.018730044111352373 0.1794348200638964 chr12 133851895 2534264 0.01893334420106641 0.1634177648085177 chr13 115169878 2696473 0.023413005612457103 0.18154978727603752 chr14 107349540 1223025 0.011392922596594265 0.1324918745807635 chr15 102531392 2424078 0.023642300691674993 0.18304114511271105 chr16 90354753 1707365 0.018896238917281972 0.17677541508985503 chr17 81195210 1197009 0.01474235980176663 0.14529521225490064 chr18 78077248 2085801 0.02671458143606701 0.3613939931485538 chr19 59128983 1057043 0.017876901417364137 0.20717434196717943 chr20 63025520 1637405 0.02598003158085804 0.19580020006017443 chr21 48129895 1203818 0.025011855936938984 0.19086160251998335 chr22 51304566 631802 0.012314732376841468 0.12957410507506142 chrMT 16571 14424 0.8704363043871824 1.1356935191976392 chrX 155270560 4163473 0.026814310452670485 0.2017851097367884 chrY 59373566 162736 0.0027408830387583593 0.07017911448587917