BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975263.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 6,540,500 number of mapped reads = 6,342,761 (96.98%) number of supplementary alignments = 91,940 (1.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,196,026 number of mapped paired reads (second in pair) = 3,146,735 number of mapped paired reads (both in pair) = 6,271,488 number of mapped paired reads (singletons) = 71,273 number of mapped bases = 872,800,861 bp number of sequenced bases = 872,104,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 832,332 duplication rate = 9.73% >>>>>>> Insert size mean insert size = 63,946.3744 std insert size = 2,422,728.2385 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.5503 >>>>>>> ACTG content number of A's = 247,087,877 bp (28.33%) number of C's = 179,973,164 bp (20.64%) number of T's = 250,110,165 bp (28.68%) number of G's = 194,857,471 bp (22.34%) number of N's = 75,611 bp (0.01%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 10,145,351 number of insertions = 170,369 mapped reads with insertion percentage = 2.48% number of deletions = 348,073 mapped reads with deletion percentage = 5.24% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.2819X std coverageData = 2.6889X There is a 12.66% of reference with a coverageData >= 1X There is a 7.2% of reference with a coverageData >= 2X There is a 3.18% of reference with a coverageData >= 3X There is a 1.78% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 68780390 0.27594872070549425 2.7508479114191426 chr2 243199373 89787111 0.3691913753412514 4.112516509038464 chr3 198022430 55923019 0.2824074979788906 0.9435031041245807 chr4 191154276 58936012 0.30831647208352275 2.5120533256003625 chr5 180915260 62825642 0.3472655761597999 1.0748238702304505 chr6 171115067 43041618 0.25153610815580607 2.009188907899982 chr7 159138663 78595541 0.4938808679070026 4.634310083435002 chr8 146364022 47590360 0.32515067124897673 1.46604279015119 chr9 141213431 37039827 0.2622967711902701 4.17203344416662 chr10 135534747 37448835 0.27630431183820336 4.991904065861268 chr11 135006516 35078942 0.2598314736156883 1.3067952842063641 chr12 133851895 32021245 0.23922892537307747 0.8622456036160759 chr13 115169878 20197035 0.17536733867166204 0.7176341353361789 chr14 107349540 29779349 0.2774054644295635 1.0187582226403473 chr15 102531392 18529764 0.1807228365728225 0.7318420466306896 chr16 90354753 20382585 0.225583982283699 2.544477467074609 chr17 81195210 24230057 0.29841732043060176 2.2482299075095353 chr18 78077248 19876148 0.254570294280864 3.8970257542290785 chr19 59128983 10676799 0.18056794584138205 1.5698220108241758 chr20 63025520 14287645 0.22669618592595508 1.1296307030405321 chr21 48129895 16259875 0.33783317000795454 1.7498483166810808 chr22 51304566 9673989 0.18856000068298015 0.8383570813786035 chrMT 16571 1132191 68.32363768028483 34.30278670013325 chrX 155270560 35659331 0.22965931854692867 1.035615003337184 chrY 59373566 5047551 0.08501343847192874 4.31815086418624