BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089378.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 29,635,251 number of mapped reads = 27,990,071 (94.45%) number of supplementary alignments = 143,494 (0.48%) number of secondary alignments = 0 number of mapped bases = 1,863,505,127 bp number of sequenced bases = 1,862,763,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,310,773 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5039 >>>>>>> ACTG content number of A's = 510,054,136 bp (27.38%) number of C's = 335,608,778 bp (18.02%) number of T's = 586,339,629 bp (31.48%) number of G's = 430,569,666 bp (23.11%) number of N's = 191,700 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,630,058 number of insertions = 133,590 mapped reads with insertion percentage = 0.47% number of deletions = 427,879 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.1% >>>>>>> Coverage mean coverageData = 0.602X std coverageData = 3.6954X There is a 19.06% of reference with a coverageData >= 1X There is a 12.01% of reference with a coverageData >= 2X There is a 7.98% of reference with a coverageData >= 3X There is a 5.43% of reference with a coverageData >= 4X There is a 3.77% of reference with a coverageData >= 5X There is a 2.67% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.41% of reference with a coverageData >= 8X There is a 1.05% of reference with a coverageData >= 9X There is a 0.79% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 143972553 0.5776216421141835 6.016279670661134 chr2 243199373 165559185 0.6807549828674928 4.31482885856935 chr3 198022430 131032996 0.661707847944296 1.957412470389738 chr4 191154276 121244734 0.6342768602257163 2.3646188664241685 chr5 180915260 117715882 0.6506686168983202 1.9623389483347908 chr6 171115067 112537288 0.6576702447832954 2.7398553214474437 chr7 159138663 102516426 0.6441955968927551 4.843579378088565 chr8 146364022 93002357 0.6354181562460752 5.136514073657162 chr9 141213431 76991092 0.5452108305476977 4.04111146307645 chr10 135534747 84650049 0.6245634486630945 3.956125812991288 chr11 135006516 86078311 0.6375863443509645 4.104618396049578 chr12 133851895 81454496 0.6085419709597686 2.07184500468007 chr13 115169878 60099108 0.5218300917189476 1.721760408166996 chr14 107349540 57771163 0.5381593903429861 2.0133601343116134 chr15 102531392 51950567 0.5066796225686666 1.836081144985473 chr16 90354753 48448831 0.5362067781868652 2.3261015463099572 chr17 81195210 46250063 0.5696156583621127 2.420616664732264 chr18 78077248 53415439 0.6841357805029193 8.054622562386472 chr19 59128983 33316100 0.5634478780059519 3.8472728383474486 chr20 63025520 35624484 0.5652390333312601 2.099814133412661 chr21 48129895 25060856 0.5206920979154432 2.425720883479773 chr22 51304566 19148681 0.37323541534295407 1.4300841101239796 chrMT 16571 247182 14.91654094502444 17.562347134599346 chrX 155270560 111019918 0.7150094518883683 2.7688018273800927 chrY 59373566 4397366 0.07406268978353094 1.4405342672262835