BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251078.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,979,674 number of mapped reads = 3,814,151 (95.84%) number of supplementary alignments = 33,382 (0.84%) number of secondary alignments = 0 number of mapped bases = 295,027,874 bp number of sequenced bases = 294,826,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 639,191 duplication rate = 14.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9122 >>>>>>> ACTG content number of A's = 86,509,759 bp (29.34%) number of C's = 58,746,695 bp (19.93%) number of T's = 87,347,856 bp (29.63%) number of G's = 62,219,766 bp (21.1%) number of N's = 2,817 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,818,569 number of insertions = 36,729 mapped reads with insertion percentage = 0.95% number of deletions = 112,566 mapped reads with deletion percentage = 2.9% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.0953X std coverageData = 1.0293X There is a 6.83% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 24002734 0.0962995955785402 2.1913390821195833 chr2 243199373 25253747 0.10383968794195864 1.2764583395055955 chr3 198022430 19300720 0.09746734246216451 0.4112821840891729 chr4 191154276 18866980 0.09870027704742529 0.49143187032832225 chr5 180915260 17965263 0.0993020876182584 0.4321913204532288 chr6 171115067 17166641 0.1003222059925325 0.6048105314136379 chr7 159138663 15871573 0.09973423617364437 1.612369675851515 chr8 146364022 14442336 0.09867408535685088 0.6915797005991606 chr9 141213431 12584163 0.089114490816387 1.1922018246501944 chr10 135534747 16690353 0.12314445829894824 1.0274904465982166 chr11 135006516 13089304 0.09695312780310544 0.6285319085751827 chr12 133851895 13236846 0.09889173403185662 0.43319269258332316 chr13 115169878 9155698 0.07949733175891703 0.3625624333807474 chr14 107349540 8811050 0.08207813466177871 0.6297118216488534 chr15 102531392 8258792 0.0805489113031841 0.3678591053892604 chr16 90354753 8115489 0.0898180641365928 0.7900376109925068 chr17 81195210 7531956 0.09276355095331362 0.5329533968758747 chr18 78077248 7828343 0.10026407436901465 1.2666422456406234 chr19 59128983 5848540 0.0989115608499473 1.874538860471414 chr20 63025520 6065977 0.09624636179122362 0.46232088395908855 chr21 48129895 3863141 0.08026489565373039 0.43130774582358467 chr22 51304566 3276116 0.0638562267537747 0.3643295544893621 chrMT 16571 144068 8.693983465089614 5.67258363491109 chrX 155270560 16710775 0.1076235894299602 0.5304539801630336 chrY 59373566 947269 0.01595438953422471 0.8728612036937686