BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173936.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,787,972 number of mapped reads = 4,681,417 (97.77%) number of supplementary alignments = 575,872 (12.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,344,590 number of mapped paired reads (second in pair) = 2,336,827 number of mapped paired reads (both in pair) = 4,614,032 number of mapped paired reads (singletons) = 67,385 number of mapped bases = 530,468,060 bp number of sequenced bases = 530,063,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,771,388 duplication rate = 65.45% >>>>>>> Insert size mean insert size = 953,427.9013 std insert size = 8,547,770.6575 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.6821 >>>>>>> ACTG content number of A's = 158,265,176 bp (29.86%) number of C's = 105,358,418 bp (19.88%) number of T's = 156,958,964 bp (29.61%) number of G's = 109,476,297 bp (20.65%) number of N's = 4,231 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 4,553,623 number of insertions = 59,246 mapped reads with insertion percentage = 1.22% number of deletions = 173,555 mapped reads with deletion percentage = 3.61% homopolymer indels = 40.7% >>>>>>> Coverage mean coverageData = 0.1714X std coverageData = 3.0949X There is a 3.53% of reference with a coverageData >= 1X There is a 2.68% of reference with a coverageData >= 2X There is a 2.03% of reference with a coverageData >= 3X There is a 1.65% of reference with a coverageData >= 4X There is a 1.25% of reference with a coverageData >= 5X There is a 1.04% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.52% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 40377256 0.16199460542166513 1.541017171514144 chr2 243199373 48922918 0.2011638327702432 9.775891880138506 chr3 198022430 35837447 0.18097670551765271 1.3117534625205949 chr4 191154276 37297342 0.1951164409212588 1.8922841534342583 chr5 180915260 34325745 0.18973382897606317 1.3481412250972775 chr6 171115067 30741845 0.17965597968062041 1.4374934997170823 chr7 159138663 29614424 0.18609194925811334 1.6953928754216108 chr8 146364022 27957044 0.1910103563565642 2.0074892617789293 chr9 141213431 22651430 0.16040563450370382 1.4228188129801909 chr10 135534747 26786036 0.19763224260122755 1.970479350068756 chr11 135006516 24191164 0.17918515873707902 1.3310544091116656 chr12 133851895 24161898 0.18051218475464992 1.3420097178140553 chr13 115169878 16661455 0.1446685130638065 1.1674469581884834 chr14 107349540 16335083 0.15216723797791776 1.2011409771005075 chr15 102531392 15233712 0.14857607707110815 1.1989734399769705 chr16 90354753 16195908 0.1792479915251387 1.513657725513166 chr17 81195210 14042770 0.1729507196298895 1.3304170320523663 chr18 78077248 14350272 0.18379582231177 1.856175715658734 chr19 59128983 10218825 0.17282260714682002 1.4030837679661632 chr20 63025520 11621559 0.184394496070798 1.4136492772648257 chr21 48129895 7454923 0.1548917362067796 1.6115885634045648 chr22 51304566 6613887 0.12891419839707835 1.1612854242659563 chrMT 16571 415151 25.05286343612335 22.597823863896345 chrX 155270560 14247067 0.09175639606117218 0.9274678521764496 chrY 59373566 4212899 0.0709558021157092 1.2960597443754873