BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251054.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 = 3,395,790 number of mapped reads = 3,263,184 (96.09%) number of supplementary alignments = 30,203 (0.89%) number of secondary alignments = 0 number of mapped bases = 253,909,735 bp number of sequenced bases = 253,750,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 789,591 duplication rate = 21.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2061 >>>>>>> ACTG content number of A's = 75,008,918 bp (29.56%) number of C's = 50,149,443 bp (19.76%) number of T's = 75,660,598 bp (29.82%) number of G's = 52,911,754 bp (20.85%) number of N's = 19,710 bp (0.01%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,517,236 number of insertions = 32,187 mapped reads with insertion percentage = 0.97% number of deletions = 89,574 mapped reads with deletion percentage = 2.7% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.082X std coverageData = 0.9163X There is a 5.3% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.22% 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 0.01% 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 20178966 0.08095853851453393 1.9689390503237605 chr2 243199373 21786414 0.08958252536284293 1.0218897857893658 chr3 198022430 16883755 0.08526183119760726 0.41926060859182124 chr4 191154276 16456135 0.08608823900962592 0.48865532019242747 chr5 180915260 15430436 0.0852909588721261 0.42892411939185293 chr6 171115067 14649106 0.08560967924583754 0.5286037803935397 chr7 159138663 13678027 0.08595037021267421 1.3412169233672728 chr8 146364022 12293644 0.08399361968886042 0.638972911413281 chr9 141213431 10565075 0.07481636077520133 0.9494295237317676 chr10 135534747 14958501 0.11036653943803798 0.9359780469220433 chr11 135006516 11325796 0.0838907360589914 0.5848748402045104 chr12 133851895 11189423 0.0835955516356343 0.425304681303853 chr13 115169878 7949941 0.06902795364600456 0.3697917037146935 chr14 107349540 7583658 0.07064453187223718 0.623665481499811 chr15 102531392 7007680 0.06834667766921569 0.36715410777233154 chr16 90354753 7085116 0.0784144249721982 0.6731166211324983 chr17 81195210 6318343 0.07781669632974654 0.5097038008885774 chr18 78077248 6754850 0.08651496015843181 1.1174398299156638 chr19 59128983 4930372 0.08338333842136267 1.9121803754324376 chr20 63025520 5121073 0.08125395871386702 0.45508869723819706 chr21 48129895 3299919 0.06856277164120138 0.4229684704724355 chr22 51304566 2715354 0.052926166454658245 0.33653340291247974 chrMT 16571 278656 16.81588316939231 9.182298012234645 chrX 155270560 14638683 0.09427854836100288 0.5098466090223791 chrY 59373566 830812 0.013992961109999693 0.7524660775929203