BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472427.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 = 15,964,632 number of mapped reads = 15,837,639 (99.2%) number of supplementary alignments = 61,311 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,940,200 number of mapped paired reads (second in pair) = 7,897,439 number of mapped paired reads (both in pair) = 15,766,730 number of mapped paired reads (singletons) = 70,909 number of mapped bases = 1,553,858,284 bp number of sequenced bases = 1,553,680,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,867,645 duplication rate = 47.71% >>>>>>> Insert size mean insert size = 16,317.161 std insert size = 1,254,849.209 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.867 >>>>>>> ACTG content number of A's = 419,696,112 bp (27.01%) number of C's = 357,843,568 bp (23.03%) number of T's = 420,765,892 bp (27.08%) number of G's = 355,175,784 bp (22.86%) number of N's = 198,787 bp (0.01%) GC percentage = 45.89% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 8,101,235 number of insertions = 92,236 mapped reads with insertion percentage = 0.58% number of deletions = 74,286 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.5019X std coverageData = 16.5933X There is a 4.16% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% 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 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% 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 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% 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 0.19% of reference with a coverageData >= 41X There is a 0.19% 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 0.18% of reference with a coverageData >= 46X There is a 0.18% 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 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154971287 0.621748850126235 22.61938221764259 chr2 243199373 111271136 0.45753052167613933 13.052764167676958 chr3 198022430 101615215 0.5131500254794369 12.108252510892305 chr4 191154276 29749970 0.15563329590388028 5.674987344551182 chr5 180915260 63475258 0.35085629592550677 10.707464470582655 chr6 171115067 149794354 0.8754013110955332 24.3583099296679 chr7 159138663 84346638 0.5300197727562912 13.208198217015356 chr8 146364022 113630837 0.7763577103668278 18.74058136755847 chr9 141213431 51139510 0.36214338563872156 9.081323541186633 chr10 135534747 22318563 0.16467041473873856 5.14706609045001 chr11 135006516 49789685 0.3687946809915456 13.239197908950912 chr12 133851895 112885454 0.8433608952641276 27.076508460932562 chr13 115169878 70265782 0.6101055520784697 25.76992823409355 chr14 107349540 34566335 0.3219979796839372 9.604728108611084 chr15 102531392 33159850 0.3234116825410895 17.470485880459613 chr16 90354753 88677924 0.9814417178474275 26.4731986113107 chr17 81195210 60715742 0.7477749241611666 18.200838063959328 chr18 78077248 9040368 0.11578748267356964 4.841331846200361 chr19 59128983 37542588 0.6349270035643941 14.543005721447864 chr20 63025520 67416063 1.069662939710771 27.009812095797145 chr21 48129895 15608375 0.3242968845039034 16.599749801906132 chr22 51304566 9173941 0.17881334382596667 5.093223140686597 chrMT 16571 7198 0.4343733027578299 0.8580754231981575 chrX 155270560 82331409 0.5302448126676429 13.1191641429257 chrY 59373566 364802 0.006144182075908999 0.6102420058916013