BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818835.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 = 975,147 number of mapped reads = 963,606 (98.82%) number of supplementary alignments = 15,600 (1.6%) number of secondary alignments = 0 number of mapped bases = 89,269,743 bp number of sequenced bases = 89,216,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,109 duplication rate = 15.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2618 >>>>>>> ACTG content number of A's = 25,174,873 bp (28.22%) number of C's = 18,446,953 bp (20.68%) number of T's = 25,624,180 bp (28.72%) number of G's = 19,969,317 bp (22.38%) number of N's = 1,331 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 517,482 number of insertions = 10,690 mapped reads with insertion percentage = 1.07% number of deletions = 27,718 mapped reads with deletion percentage = 2.82% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.338X There is a 2.17% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 8363928 0.03355629753877323 0.45683660715915064 chr2 243199373 6749833 0.027754319086998634 0.4553168639204212 chr3 198022430 5630157 0.028431915515833232 0.2124194289381714 chr4 191154276 4555024 0.02382904581218994 0.23024914193210833 chr5 180915260 3929352 0.02171929554201232 0.19302727724904548 chr6 171115067 4490664 0.026243533539919078 0.21693679380953199 chr7 159138663 8056608 0.050626339621817736 0.6581481787937871 chr8 146364022 7773831 0.05311299111471534 0.3450174925430356 chr9 141213431 3296245 0.023342291003466943 0.29512354556995674 chr10 135534747 4089764 0.030175022202977957 0.46679040767266194 chr11 135006516 3911463 0.0289724015987495 0.23862741916391694 chr12 133851895 3512088 0.026238612460436215 0.20857165583076168 chr13 115169878 2617440 0.022726775832826705 0.18935608946199123 chr14 107349540 2673921 0.024908546417618558 0.2090029316409795 chr15 102531392 2483817 0.024224941762226344 0.19438335201681073 chr16 90354753 2249679 0.02489829173679441 0.35071037041912545 chr17 81195210 2218663 0.02732504786920312 0.24620803713549136 chr18 78077248 1686341 0.02159836627438508 0.3310757090779748 chr19 59128983 1476211 0.02496594605728294 0.4052787834438223 chr20 63025520 3683817 0.058449608983789425 0.3216841137884922 chr21 48129895 849423 0.017648552941991667 0.18487342575302165 chr22 51304566 816215 0.015909207769148656 0.18175079403384778 chrMT 16571 178824 10.791382535755234 7.523805567415101 chrX 155270560 3679528 0.023697525145784236 0.21973262119082057 chrY 59373566 296907 0.0050006597211964664 0.36989098204669607