BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618655.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 59,291,343 number of mapped reads = 53,031,208 (89.44%) number of supplementary alignments = 321,703 (0.54%) number of secondary alignments = 0 number of mapped bases = 4,910,179,763 bp number of sequenced bases = 4,906,012,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,317,462 duplication rate = 48.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8593 >>>>>>> ACTG content number of A's = 1,284,843,727 bp (26.19%) number of C's = 1,189,144,736 bp (24.24%) number of T's = 1,529,684,845 bp (31.18%) number of G's = 900,296,789 bp (18.35%) number of N's = 2,042,489 bp (0.04%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 62,621,080 number of insertions = 1,230,043 mapped reads with insertion percentage = 2.23% number of deletions = 2,374,110 mapped reads with deletion percentage = 4.33% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 1.5861X std coverageData = 177.682X There is a 13.22% of reference with a coverageData >= 1X There is a 8.59% of reference with a coverageData >= 2X There is a 6.35% of reference with a coverageData >= 3X There is a 4.99% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 3.48% of reference with a coverageData >= 6X There is a 3.03% of reference with a coverageData >= 7X There is a 2.68% of reference with a coverageData >= 8X There is a 2.41% of reference with a coverageData >= 9X There is a 2.19% of reference with a coverageData >= 10X There is a 2% of reference with a coverageData >= 11X There is a 1.85% of reference with a coverageData >= 12X There is a 1.72% of reference with a coverageData >= 13X There is a 1.6% of reference with a coverageData >= 14X There is a 1.5% of reference with a coverageData >= 15X There is a 1.41% of reference with a coverageData >= 16X There is a 1.34% of reference with a coverageData >= 17X There is a 1.27% of reference with a coverageData >= 18X There is a 1.2% of reference with a coverageData >= 19X There is a 1.15% of reference with a coverageData >= 20X There is a 1.09% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 1% of reference with a coverageData >= 23X There is a 0.96% of reference with a coverageData >= 24X There is a 0.92% of reference with a coverageData >= 25X There is a 0.89% of reference with a coverageData >= 26X There is a 0.86% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.7% of reference with a coverageData >= 33X There is a 0.68% of reference with a coverageData >= 34X There is a 0.66% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.63% of reference with a coverageData >= 37X There is a 0.61% of reference with a coverageData >= 38X There is a 0.59% of reference with a coverageData >= 39X There is a 0.58% of reference with a coverageData >= 40X There is a 0.57% of reference with a coverageData >= 41X There is a 0.55% of reference with a coverageData >= 42X There is a 0.54% of reference with a coverageData >= 43X There is a 0.53% of reference with a coverageData >= 44X There is a 0.51% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.48% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 447487066 1.7953297937821386 43.024099701655174 chr2 243199373 445164317 1.8304501015304837 67.82604062876938 chr3 198022430 311275259 1.5719191962243872 27.88326491368731 chr4 191154276 352994918 1.8466493420215198 684.3202322437023 chr5 180915260 302495704 1.6720297889741307 29.094868998889826 chr6 171115067 271710004 1.587878897888051 25.451040012028155 chr7 159138663 230789525 1.4502416989641291 25.793714718030333 chr8 146364022 252553200 1.72551421140914 30.524289285266814 chr9 141213431 210458355 1.4903565015710156 37.593119787937376 chr10 135534747 255968891 1.8885850061755751 158.38313248288821 chr11 135006516 258898033 1.9176706478374719 30.82670873267035 chr12 133851895 233576165 1.7450344277905068 32.83016087887283 chr13 115169878 138337635 1.201161600605325 24.38422185365193 chr14 107349540 142858502 1.3307788929510085 21.978652263653217 chr15 102531392 158699524 1.5478140002234633 29.11637388607392 chr16 90354753 179669311 1.9884876559841849 62.17718757620924 chr17 81195210 137727197 1.6962478082143022 29.58327570578154 chr18 78077248 120167292 1.5390820639579919 23.173522666593325 chr19 59128983 100379876 1.697642524986435 41.83981957298192 chr20 63025520 136711487 2.1691449273246772 32.27818907213581 chr21 48129895 60620843 1.2595257687555728 56.5430025191496 chr22 51304566 69037220 1.345635006443676 99.4841890028885 chrMT 16571 4823 0.2910506306197574 1.0601044427757067 chrX 155270560 11931295 0.07684196540541878 6.959969132103669 chrY 59373566 80663321 1.3585729548398693 100.24169967863318