BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008771.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 = 7,286,491 number of mapped reads = 6,676,107 (91.62%) number of supplementary alignments = 30,257 (0.42%) number of secondary alignments = 0 number of mapped bases = 443,888,534 bp number of sequenced bases = 443,707,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,348 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0771 >>>>>>> ACTG content number of A's = 122,628,447 bp (27.64%) number of C's = 80,812,169 bp (18.21%) number of T's = 140,383,820 bp (31.64%) number of G's = 99,801,192 bp (22.49%) number of N's = 81,689 bp (0.02%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 3,060,674 number of insertions = 37,835 mapped reads with insertion percentage = 0.56% number of deletions = 109,207 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.1434X std coverageData = 1.0543X There is a 9.51% of reference with a coverageData >= 1X There is a 2.85% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 40478802 0.16240201062528145 1.7323843018993446 chr2 243199373 38871844 0.15983529694379597 1.2833159486396566 chr3 198022430 34062972 0.17201572569329646 0.6181029598147285 chr4 191154276 21810612 0.1140995245118137 0.5375444982378664 chr5 180915260 18925981 0.10461240804120117 0.4497519984235464 chr6 171115067 24426068 0.14274644792091862 0.7133966232771997 chr7 159138663 27864853 0.17509794587126826 1.721789382450389 chr8 146364022 39960415 0.27302074959377653 1.1821598211311133 chr9 141213431 11731179 0.08307410220774254 0.9895900840041241 chr10 135534747 23063269 0.17016499097460225 1.3089647722054805 chr11 135006516 20677591 0.1531599482205733 1.3166306966019021 chr12 133851895 18637027 0.13923618339508753 0.5311927675810556 chr13 115169878 12756603 0.11076336296891796 0.45603346267670136 chr14 107349540 15361764 0.14310041757048983 0.5664602240677931 chr15 102531392 10825371 0.1055810399999251 0.4558245677112006 chr16 90354753 10050785 0.11123692629650594 0.683265378016123 chr17 81195210 12358480 0.15220700827056177 0.9208150305453453 chr18 78077248 6125885 0.07845928432313598 1.960501348780435 chr19 59128983 9250758 0.15645048385154875 1.1300645879063422 chr20 63025520 9563489 0.15173994597743898 0.5822178153332757 chr21 48129895 3999918 0.083106726079498 0.48503865228809534 chr22 51304566 5020774 0.097862127904951 0.42778437363943106 chrMT 16571 105950 6.3936998370647515 4.8063704586305915 chrX 155270560 26790680 0.1725419165101227 0.7669620996689082 chrY 59373566 1167464 0.019663026472083553 0.453751303888049