BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080688.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,588,398 number of mapped reads = 2,283,988 (88.24%) number of supplementary alignments = 24,930 (0.96%) number of secondary alignments = 0 number of mapped bases = 162,534,571 bp number of sequenced bases = 162,473,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,286 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2563 >>>>>>> ACTG content number of A's = 49,608,681 bp (30.53%) number of C's = 29,967,589 bp (18.44%) number of T's = 50,534,069 bp (31.1%) number of G's = 32,360,651 bp (19.92%) number of N's = 2,477 bp (0%) GC percentage = 38.36% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,290,105 number of insertions = 12,518 mapped reads with insertion percentage = 0.54% number of deletions = 33,683 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0525X std coverageData = 0.4639X There is a 3.45% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 12469114 0.05002641096729705 0.42158717462820194 chr2 243199373 14469189 0.059495173945205856 0.4163955838152333 chr3 198022430 11021695 0.055658821073956116 0.3333749952007111 chr4 191154276 11298279 0.05910555199926577 0.35689973121757723 chr5 180915260 10204586 0.056405335846185664 0.3371679081440483 chr6 171115067 10384201 0.06068548598353411 0.37943818835059057 chr7 159138663 8548718 0.05371867426082372 0.4437822830728997 chr8 146364022 8743271 0.05973647676886059 1.3595508526149749 chr9 141213431 6502942 0.046050449691290345 0.37540444518051586 chr10 135534747 7480357 0.05519143367715144 0.3903978376472198 chr11 135006516 7225601 0.053520387119685396 0.380335642682578 chr12 133851895 7866075 0.05876700512906448 0.34378347589335123 chr13 115169878 5854871 0.05083682558038309 0.3200999441054774 chr14 107349540 5150091 0.04797497036317063 0.3211007545919803 chr15 102531392 4246335 0.04141497464503359 0.2832549251332227 chr16 90354753 3731653 0.04130001882690112 0.2923873806972027 chr17 81195210 3569215 0.04395844286873573 0.2992961586255504 chr18 78077248 4425398 0.05667973850717689 0.49747714792156184 chr19 59128983 2222263 0.03758331172379542 0.33843165071065767 chr20 63025520 2711785 0.04302677708966146 0.2940768637052828 chr21 48129895 2240617 0.04655354016459001 0.31644468495830896 chr22 51304566 1344714 0.026210415657740873 0.21875659298097125 chrMT 16571 164648 9.93591213565868 6.642109078683078 chrX 155270560 10255561 0.06604961687521446 0.36927251959883367 chrY 59373566 403392 0.006794134615394332 0.1608122332297804