BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472614.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,078,684 number of mapped reads = 17,943,823 (99.25%) number of supplementary alignments = 81,845 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,996,332 number of mapped paired reads (second in pair) = 8,947,491 number of mapped paired reads (both in pair) = 17,850,440 number of mapped paired reads (singletons) = 93,383 number of mapped bases = 1,766,607,430 bp number of sequenced bases = 1,766,391,669 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,299,850 duplication rate = 50.37% >>>>>>> Insert size mean insert size = 19,602.0094 std insert size = 1,373,982.2525 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 54.9405 >>>>>>> ACTG content number of A's = 465,992,479 bp (26.38%) number of C's = 419,879,479 bp (23.77%) number of T's = 466,428,032 bp (26.41%) number of G's = 413,760,659 bp (23.42%) number of N's = 331,020 bp (0.02%) GC percentage = 47.19% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,929,533 number of insertions = 104,096 mapped reads with insertion percentage = 0.57% number of deletions = 87,891 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.5707X std coverageData = 23.9538X There is a 3.49% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 240976939 0.9668057717697722 29.097677211618418 chr2 243199373 77427047 0.31836861273486916 13.080176727261861 chr3 198022430 174889671 0.8831811174118003 27.27997869459322 chr4 191154276 42882175 0.22433280540373576 11.233421549148687 chr5 180915260 158086325 0.8738142100340237 59.7608707546345 chr6 171115067 150938703 0.8820889103821582 23.588015759792626 chr7 159138663 84191400 0.5290442838520014 18.196025374835926 chr8 146364022 67764724 0.46298757764391035 13.133251897985112 chr9 141213431 82521306 0.5843729269633 18.324599746138436 chr10 135534747 26280908 0.19390531639831077 9.203272774472461 chr11 135006516 48746878 0.36107055751294254 17.356193538048117 chr12 133851895 97972340 0.7319458570235409 22.291732996178432 chr13 115169878 65304157 0.567024626005074 21.31936981463748 chr14 107349540 33278277 0.3099992510447646 18.40935023285213 chr15 102531392 32679690 0.3187286289841847 12.886276102008656 chr16 90354753 76331892 0.8448021765938534 28.9747609581029 chr17 81195210 49595788 0.6108215989588548 14.726531808459802 chr18 78077248 38669761 0.4952756659660955 20.557531087745584 chr19 59128983 33295676 0.5631024636429144 14.11807140562841 chr20 63025520 59431804 0.9429799865197462 26.366592091576308 chr21 48129895 7085446 0.14721507287726265 7.695401529326152 chr22 51304566 22878178 0.44592869180493605 17.685920625553837 chrMT 16571 450 0.027155874720897956 0.1899311857279546 chrX 155270560 94621530 0.6093977506102896 19.632974831969314 chrY 59373566 756365 0.012739086616424556 0.42209783740414175