BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124952.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,319,778 number of mapped reads = 4,252,929 (98.45%) number of supplementary alignments = 19,598 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,130,987 number of mapped paired reads (second in pair) = 2,121,942 number of mapped paired reads (both in pair) = 4,233,606 number of mapped paired reads (singletons) = 19,323 number of mapped bases = 370,042,577 bp number of sequenced bases = 369,842,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 352,184 duplication rate = 5.51% >>>>>>> Insert size mean insert size = 38,479.943 std insert size = 1,809,689.2655 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6431 >>>>>>> ACTG content number of A's = 104,884,552 bp (28.36%) number of C's = 67,750,881 bp (18.32%) number of T's = 111,992,081 bp (30.28%) number of G's = 85,209,829 bp (23.04%) number of N's = 5,595 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,773,802 number of insertions = 49,621 mapped reads with insertion percentage = 1.14% number of deletions = 120,471 mapped reads with deletion percentage = 2.78% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.1195X std coverageData = 1.2624X There is a 8.26% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 26418507 0.10599173993632698 1.4114344041342302 chr2 243199373 27465664 0.11293476484415114 1.4703356958769815 chr3 198022430 37043350 0.1870664348478099 0.640815365268356 chr4 191154276 28069978 0.14684462512363575 0.6970398370384657 chr5 180915260 22142337 0.12239065405538482 0.45663179299984785 chr6 171115067 21576738 0.1260949043137154 1.775514583645296 chr7 159138663 21562964 0.1354979587832782 1.7259859681037393 chr8 146364022 25683640 0.17547782336836848 0.6981007252935345 chr9 141213431 15770827 0.11168078622776328 1.8156463588580753 chr10 135534747 16832439 0.12419279463442684 2.5844358968681913 chr11 135006516 17570415 0.13014494055975787 1.0810103298118787 chr12 133851895 14078186 0.10517733798240211 0.4155399582050885 chr13 115169878 10020793 0.08700880103389534 0.38267474730448636 chr14 107349540 13114714 0.12216832973853452 0.5529563264498994 chr15 102531392 6566163 0.06404051356290959 0.3250424258191302 chr16 90354753 10109748 0.11188949849710729 2.009253245588983 chr17 81195210 5622917 0.06925183148119206 0.7742273333089635 chr18 78077248 12167995 0.1558455928159763 1.9678831321269517 chr19 59128983 7073523 0.11962869376596584 0.9699190085605229 chr20 63025520 8081122 0.1282198385669805 0.490113158528856 chr21 48129895 4612903 0.09584278129009008 0.4925313247555077 chr22 51304566 2948801 0.057476385240253274 0.3195434222137169 chrMT 16571 174789 10.547884859091184 8.017274280357883 chrX 155270560 10744650 0.06919953145013452 0.5861235668000326 chrY 59373566 4589414 0.07729726053510076 1.5322756262672472