BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514700.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 38,792,105 number of mapped reads = 38,312,785 (98.76%) number of supplementary alignments = 5,205,563 (13.42%) number of secondary alignments = 0 number of mapped bases = 3,541,726,647 bp number of sequenced bases = 3,533,748,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,705,752 duplication rate = 41.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6045 >>>>>>> ACTG content number of A's = 966,254,437 bp (27.34%) number of C's = 789,863,244 bp (22.35%) number of T's = 966,704,321 bp (27.36%) number of G's = 808,081,469 bp (22.87%) number of N's = 2,844,750 bp (0.08%) GC percentage = 45.22% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 37,052,049 number of insertions = 2,621,567 mapped reads with insertion percentage = 6.46% number of deletions = 2,605,688 mapped reads with deletion percentage = 6.23% homopolymer indels = 21.78% >>>>>>> Coverage mean coverageData = 1.1441X std coverageData = 437.4196X There is a 3.3% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 156661395 0.6285296075551202 32.543642755762846 chr2 243199373 447195975 1.8388039799757214 478.3562609277607 chr3 198022430 116533279 0.5884852488680197 21.55866038876719 chr4 191154276 174343689 0.9120574891037226 42.66658934430337 chr5 180915260 101692371 0.5620994657940961 23.28233148000512 chr6 171115067 145352374 0.8494422878611853 47.722710205328674 chr7 159138663 103282788 0.6490112839517823 32.13911178795062 chr8 146364022 147569331 1.0082350087373249 97.91346940281622 chr9 141213431 61296728 0.43407151547787265 16.04877908532743 chr10 135534747 234231202 1.7282003853963737 201.5570319207224 chr11 135006516 95814938 0.709706026337277 25.9839949644336 chr12 133851895 240629459 1.797729191656196 297.85657924870765 chr13 115169878 398548807 3.460529905224003 997.7535960591085 chr14 107349540 696423854 6.487441436637735 1930.4779026484725 chr15 102531392 68885077 0.6718437705400508 34.79520833043811 chr16 90354753 44501936 0.4925245714522622 20.724510413161582 chr17 81195210 24448977 0.3011135385942102 11.556126521518914 chr18 78077248 50194889 0.6428875285153494 24.144727803768756 chr19 59128983 54016052 0.9135291909214809 58.531450203744335 chr20 63025520 37249555 0.5910233664077662 39.89925306983763 chr21 48129895 33961515 0.7056220463393905 35.20968460462755 chr22 51304566 40731820 0.7939219288981023 142.1446723088787 chrMT 16571 1254969 75.73284653913463 47.823541715368144 chrX 155270560 56325755 0.36275875478261943 19.16225376044402 chrY 59373566 10579912 0.1781922952042328 5.147636798854297