BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230336.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 = 2,179,059 number of mapped reads = 1,624,753 (74.56%) number of supplementary alignments = 13,818 (0.63%) number of secondary alignments = 0 number of mapped bases = 107,365,484 bp number of sequenced bases = 107,317,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,099 duplication rate = 5.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1647 >>>>>>> ACTG content number of A's = 29,281,321 bp (27.28%) number of C's = 19,023,026 bp (17.73%) number of T's = 35,133,465 bp (32.74%) number of G's = 23,676,828 bp (22.06%) number of N's = 202,418 bp (0.19%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,110,225 number of insertions = 10,257 mapped reads with insertion percentage = 0.63% number of deletions = 29,525 mapped reads with deletion percentage = 1.8% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.4122X There is a 2.62% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11522073 0.04622685774572253 0.6934774561715802 chr2 243199373 5623843 0.023124414058419467 0.5092404082852742 chr3 198022430 3507628 0.01771328631812063 0.16626331608718883 chr4 191154276 9969233 0.05215281189943143 0.32155605132889387 chr5 180915260 6744695 0.03728096236879078 0.24396628911301813 chr6 171115067 3909475 0.022847052971670813 0.21811468728301567 chr7 159138663 6589597 0.041407894698725724 0.786738771165617 chr8 146364022 4145599 0.028323893695678847 0.5445485864996057 chr9 141213431 6230045 0.04411793521255071 0.43003603101210625 chr10 135534747 3371723 0.02487718518410633 0.3098342096991348 chr11 135006516 5445684 0.040336453093864 0.370247789996699 chr12 133851895 3004094 0.02244341777903107 0.19727833694282051 chr13 115169878 1491047 0.012946501514918683 0.14058069078932595 chr14 107349540 3354838 0.03125153587057755 0.236526942233404 chr15 102531392 4036135 0.03936487080951754 0.24848010048755817 chr16 90354753 1530791 0.01694200857369396 0.18209189270911197 chr17 81195210 3879679 0.0477821167036824 0.3197811511892337 chr18 78077248 5491333 0.07033205115016349 0.530511497363439 chr19 59128983 1968401 0.0332899519005764 0.47550742213165115 chr20 63025520 4809044 0.07630312292544353 0.3509460600592117 chr21 48129895 803675 0.01669804183034266 0.21067973230903683 chr22 51304566 690687 0.01346248597054695 0.14263457872516247 chrMT 16571 170109 10.265463761993844 6.3061424071291565 chrX 155270560 8757940 0.05640438213142272 0.33060913359862365 chrY 59373566 318116 0.005357872558976835 0.1753470626812903