BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,079,036 number of mapped reads = 1,046,825 (97.01%) number of supplementary alignments = 6,933 (0.64%) number of secondary alignments = 0 number of mapped bases = 71,155,170 bp number of sequenced bases = 71,124,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,203 duplication rate = 30.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7248 >>>>>>> ACTG content number of A's = 19,495,904 bp (27.41%) number of C's = 14,644,152 bp (20.59%) number of T's = 20,914,156 bp (29.4%) number of G's = 16,066,088 bp (22.59%) number of N's = 4,210 bp (0.01%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 361,534 number of insertions = 9,331 mapped reads with insertion percentage = 0.88% number of deletions = 18,276 mapped reads with deletion percentage = 1.73% homopolymer indels = 38.37% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.3313X There is a 1.31% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% 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 5906288 0.023696181683735905 0.4321679801795999 chr2 243199373 6351797 0.026117653683260113 0.5778181976022222 chr3 198022430 4793154 0.02420510646192959 0.24735923189837813 chr4 191154276 4680543 0.024485682967405865 0.2758900495202675 chr5 180915260 4289399 0.023709437224919555 0.2578322463437431 chr6 171115067 4205204 0.024575299380270237 0.2710567508760837 chr7 159138663 3979727 0.025007920294014285 0.28624179497370833 chr8 146364022 3546814 0.02423282683499911 0.2697386810725453 chr9 141213431 3082242 0.021826833171414126 0.2708881240492519 chr10 135534747 3388916 0.025004038263339214 0.33915770590805217 chr11 135006516 3401272 0.025193391406382194 0.282623826689659 chr12 133851895 3225464 0.02409726063273142 0.2656508414580616 chr13 115169878 2277986 0.01977935584858395 0.22353137140534293 chr14 107349540 2180153 0.020308917951581348 0.25594330978462404 chr15 102531392 2024330 0.01974351425951576 0.22767973094331737 chr16 90354753 2184763 0.024179834789654065 0.3977666776947189 chr17 81195210 1954685 0.024073895492110926 0.2638190950544834 chr18 78077248 1920185 0.024593400115741786 0.32870031684073825 chr19 59128983 1470596 0.024870984166935527 0.35990505360416 chr20 63025520 1547891 0.024559749764857156 0.2677192109729703 chr21 48129895 972313 0.020201851676593104 0.23478317394212744 chr22 51304566 868736 0.016932917822557937 0.22940413768795162 chrMT 16571 111511 6.729286102226782 6.9061484331662815 chrX 155270560 2153353 0.013868392050624408 0.20292257490155435 chrY 59373566 637848 0.01074296261740452 0.5638269952019471