BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819000.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 = 1,451,457 number of mapped reads = 1,427,460 (98.35%) number of supplementary alignments = 24,405 (1.68%) number of secondary alignments = 0 number of mapped bases = 131,920,820 bp number of sequenced bases = 131,839,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 499,854 duplication rate = 30.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1158 >>>>>>> ACTG content number of A's = 37,307,250 bp (28.3%) number of C's = 27,685,639 bp (21%) number of T's = 38,112,255 bp (28.91%) number of G's = 28,728,154 bp (21.79%) number of N's = 6,202 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 835,686 number of insertions = 21,089 mapped reads with insertion percentage = 1.44% number of deletions = 43,285 mapped reads with deletion percentage = 2.96% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.5467X There is a 2.42% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% 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 14321629 0.05745874952102928 1.0635954520068687 chr2 243199373 11145759 0.045829719306060876 0.770795447799058 chr3 198022430 6746130 0.03406750437311571 0.29035467886317895 chr4 191154276 7033607 0.036795446835832225 0.3643577501009885 chr5 180915260 6903328 0.03815779829739072 0.31777393319562147 chr6 171115067 5227110 0.030547339235767006 0.3313218428246069 chr7 159138663 6152745 0.03866279183205153 0.5385064060224157 chr8 146364022 11875569 0.08113721417138975 0.5112222329314384 chr9 141213431 5729707 0.04057480198183132 0.47478453142431976 chr10 135534747 7178070 0.05296110524336611 0.6802642627805102 chr11 135006516 4566561 0.033824745170077566 0.3603270506871935 chr12 133851895 5993940 0.04478038954921034 0.34025905661839245 chr13 115169878 2879645 0.025003456198850884 0.24473078205605556 chr14 107349540 3081970 0.028709671229145462 0.2819479161820481 chr15 102531392 3291820 0.03210548433790892 0.2802243105976396 chr16 90354753 4510365 0.04991840329639327 0.6074102467576727 chr17 81195210 4526945 0.055753843114636936 0.4110280281888548 chr18 78077248 3079880 0.03944657475632338 0.5590252285587299 chr19 59128983 2709160 0.04581780139868125 0.8404051701804808 chr20 63025520 3677885 0.05835548837994514 0.40348675620871166 chr21 48129895 1812473 0.03765794627227007 0.32854905242380544 chr22 51304566 1015499 0.01979354040340191 0.2488020673683468 chrMT 16571 49379 2.9798443063182667 3.427954170092936 chrX 155270560 7864526 0.050650464582596984 0.43227380700548174 chrY 59373566 547118 0.009214841500340404 0.6128627051396797