BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818763.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 = 1,552,012 number of mapped reads = 1,482,421 (95.52%) number of supplementary alignments = 13,593 (0.88%) number of secondary alignments = 0 number of mapped bases = 100,497,176 bp number of sequenced bases = 100,454,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 726,065 duplication rate = 41.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7949 >>>>>>> ACTG content number of A's = 28,466,102 bp (28.34%) number of C's = 22,924,664 bp (22.82%) number of T's = 29,255,542 bp (29.12%) number of G's = 19,802,322 bp (19.71%) number of N's = 6,255 bp (0.01%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 541,491 number of insertions = 12,488 mapped reads with insertion percentage = 0.83% number of deletions = 26,521 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.4427X There is a 1.4% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 8215839 0.032962160603804476 0.5990055243910353 chr2 243199373 8990636 0.03696817096646051 0.6801944495878782 chr3 198022430 6896976 0.034829266563388805 0.3593659174080344 chr4 191154276 6734923 0.035232918357526045 0.39857949322564223 chr5 180915260 6255551 0.034577243511686076 0.36488781819180155 chr6 171115067 5956879 0.03481212440515247 0.3837571144917723 chr7 159138663 5493110 0.03451775889307302 0.41601131927796775 chr8 146364022 5174215 0.03535168635909718 0.4034160844255018 chr9 141213431 4350799 0.03081009341101556 0.3795894926808229 chr10 135534747 4820479 0.03556637029764773 0.4495814057950783 chr11 135006516 4672980 0.034612996012725786 0.3890555990700852 chr12 133851895 4584535 0.03425080384554884 0.38485272425625766 chr13 115169878 3259518 0.028301827323286736 0.3224437935099511 chr14 107349540 3068103 0.02858049508176747 0.3532790008641467 chr15 102531392 2926051 0.028538098848789648 0.33004046280187904 chr16 90354753 2900662 0.03210303723590501 0.48763775328204934 chr17 81195210 2636397 0.03246985875151995 0.36588213368228584 chr18 78077248 2777308 0.03557128447969887 0.49306978052669515 chr19 59128983 1992950 0.03370512900585488 0.5146472810080175 chr20 63025520 2084087 0.033067351130145375 0.3624201046979738 chr21 48129895 1413725 0.029373116230567303 0.34653237717484586 chr22 51304566 1146860 0.022353955786313443 0.2999360365181282 chrMT 16571 71582 4.319715165047372 4.534588711766175 chrX 155270560 3134341 0.020186318642761384 0.29398771384607 chrY 59373566 938670 0.01580956077322356 0.6350740628290722