BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240232.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,547,426 number of mapped reads = 1,805,896 (70.89%) number of supplementary alignments = 13,774 (0.54%) number of secondary alignments = 0 number of mapped bases = 116,504,850 bp number of sequenced bases = 116,448,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 285,374 duplication rate = 12.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7102 >>>>>>> ACTG content number of A's = 32,303,756 bp (27.74%) number of C's = 20,856,823 bp (17.91%) number of T's = 37,863,642 bp (32.52%) number of G's = 25,380,692 bp (21.8%) number of N's = 43,195 bp (0.04%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,038,243 number of insertions = 8,304 mapped reads with insertion percentage = 0.46% number of deletions = 32,696 mapped reads with deletion percentage = 1.79% homopolymer indels = 48.01% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.4245X There is a 1.81% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 8916164 0.035771882791016195 0.6164930312335722 chr2 243199373 13501648 0.055516787866060825 0.506601449103756 chr3 198022430 7174509 0.03623078961307565 0.34751942198055147 chr4 191154276 7357227 0.03848842492019378 0.3817040043528224 chr5 180915260 5925422 0.03275247206896754 0.3249103731491587 chr6 171115067 7779490 0.04546350088505064 0.4207924273440164 chr7 159138663 7091602 0.04456240781663473 0.5157109930221436 chr8 146364022 6402531 0.043743885365489614 0.5471378110036439 chr9 141213431 4033111 0.02856039238930467 0.3666460088981142 chr10 135534747 5317355 0.03923241174456909 0.42329393601583887 chr11 135006516 4780570 0.03540992051079964 0.3866030949653581 chr12 133851895 6001721 0.044838520963786134 0.38185289785601817 chr13 115169878 3154228 0.02738761258390844 0.30674503604947156 chr14 107349540 3605897 0.03359024174672756 0.3414614951176734 chr15 102531392 3144772 0.03067130893921737 0.3628301127139997 chr16 90354753 3350219 0.03707850321941558 0.34701814648963014 chr17 81195210 2608787 0.03212981406169157 0.32698806582400286 chr18 78077248 2558548 0.032769443923023514 0.5318175602461265 chr19 59128983 1993816 0.0337197749536805 0.4284342479916516 chr20 63025520 2207827 0.0350306828091224 0.3364587657715958 chr21 48129895 1738530 0.03612162461605204 0.3472319465066812 chr22 51304566 951119 0.01853868133296362 0.23745317875543145 chrMT 16571 34887 2.105304447528815 2.383206654194317 chrX 155270560 6523671 0.04201486102710005 0.38879958442733414 chrY 59373566 351199 0.005915073384677619 0.14568999192341073