BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714117.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 638,310 number of mapped reads = 488,668 (76.56%) number of supplementary alignments = 14,746 (2.31%) number of secondary alignments = 0 number of mapped bases = 63,157,593 bp number of sequenced bases = 61,610,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,668 duplication rate = 44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6813 >>>>>>> ACTG content number of A's = 16,826,797 bp (27.31%) number of C's = 12,712,150 bp (20.63%) number of T's = 15,958,794 bp (25.9%) number of G's = 16,111,870 bp (26.15%) number of N's = 434 bp (0%) GC percentage = 46.78% >>>>>>> Mismatches and indels general error rate = 0.0473 number of mismatches = 2,726,735 number of insertions = 68,004 mapped reads with insertion percentage = 13.31% number of deletions = 242,015 mapped reads with deletion percentage = 46% homopolymer indels = 30.62% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 5.448X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% 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 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4017070 0.01611658973559789 2.305721345373351 chr2 243199373 8565707 0.03522092550789594 13.651202433636124 chr3 198022430 5002035 0.025259941512686214 11.09146031949115 chr4 191154276 2122882 0.011105595147659684 1.341296045526301 chr5 180915260 3390867 0.018742846789154215 3.0506174408647144 chr6 171115067 2547138 0.014885527292579092 2.110410637924038 chr7 159138663 2471660 0.015531486525056454 2.3440998095776067 chr8 146364022 3329075 0.02274517299066843 4.554545642764633 chr9 141213431 1888842 0.013375795677678846 1.9362948370037523 chr10 135534747 3461901 0.02554253486008278 3.894080506812984 chr11 135006516 2893454 0.02143195814341287 2.475305123044974 chr12 133851895 2830642 0.021147567615684485 3.5810959943559983 chr13 115169878 1737830 0.015089275339859265 2.3871992044954884 chr14 107349540 2180436 0.020311554199487023 2.8774056339314638 chr15 102531392 1847308 0.018016999125497098 2.3429498109478564 chr16 90354753 1599875 0.017706594804149375 2.1417116423191382 chr17 81195210 1419162 0.017478395585158287 2.689240317243193 chr18 78077248 1560347 0.019984656733802914 2.4280100837193053 chr19 59128983 1099354 0.018592472662687265 2.324762863174132 chr20 63025520 1580194 0.025072288177868267 2.9259520735499436 chr21 48129895 561507 0.011666491273251272 2.5335862885180003 chr22 51304566 628097 0.01224251658224728 2.076322906812685 chrMT 16571 65303 3.9408001931084424 25.232059149947048 chrX 155270560 6087198 0.0392038130087249 5.061336909096401 chrY 59373566 269709 0.004542577078829996 1.2953119450812864