BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081245.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,508,097 number of mapped reads = 1,344,484 (89.15%) number of supplementary alignments = 11,575 (0.77%) number of secondary alignments = 0 number of mapped bases = 87,913,359 bp number of sequenced bases = 87,877,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,748 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5757 >>>>>>> ACTG content number of A's = 25,756,125 bp (29.31%) number of C's = 16,854,324 bp (19.18%) number of T's = 26,656,140 bp (30.33%) number of G's = 18,600,464 bp (21.17%) number of N's = 10,770 bp (0.01%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 821,017 number of insertions = 6,651 mapped reads with insertion percentage = 0.49% number of deletions = 21,544 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2731X There is a 2.55% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 9365921 0.0375763196192799 0.5014701174669248 chr2 243199373 5932850 0.024395005327583638 0.26871951907274283 chr3 198022430 5978596 0.030191509113386802 0.18897246757485497 chr4 191154276 3980014 0.020820951972845222 0.16244803154812912 chr5 180915260 5276318 0.02916458235750815 0.18505893998416692 chr6 171115067 6414933 0.037489001479922276 0.23931669865407343 chr7 159138663 5811799 0.03652034578171616 0.38805423530624855 chr8 146364022 5535463 0.037819833893332065 0.39044203406857747 chr9 141213431 2375057 0.016818917175095052 0.1958709018257081 chr10 135534747 2708464 0.019983539719154085 0.24095972615026792 chr11 135006516 4903586 0.036321106160535244 0.3043238299533585 chr12 133851895 2437046 0.01820703397587311 0.14908002403140957 chr13 115169878 2707529 0.023509002935646072 0.16559752821206383 chr14 107349540 3320596 0.0309325591893547 0.19719841975657518 chr15 102531392 1578320 0.01539352942755327 0.137743367864352 chr16 90354753 2903102 0.03213004190272093 0.20377514502649527 chr17 81195210 1395734 0.017189856396701234 0.16193462021896649 chr18 78077248 2257926 0.028919128911920666 0.3541566074416185 chr19 59128983 2124024 0.03592187607894423 0.36616148579023955 chr20 63025520 2090988 0.03317684645838702 0.19902233499905017 chr21 48129895 1420747 0.029519013079085256 0.19346879925610208 chr22 51304566 533844 0.010405389648944696 0.10898854799701624 chrMT 16571 18374 1.1088045380483977 1.237001164634181 chrX 155270560 6608193 0.042559214058350794 0.24056577310771837 chrY 59373566 233935 0.003940053053239214 0.08384772692361059