BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714172.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 = 972,392 number of mapped reads = 811,626 (83.47%) number of supplementary alignments = 24,121 (2.48%) number of secondary alignments = 0 number of mapped bases = 104,253,540 bp number of sequenced bases = 102,048,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 741,491 duplication rate = 44.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.5454 >>>>>>> ACTG content number of A's = 27,056,579 bp (26.51%) number of C's = 22,700,226 bp (22.24%) number of T's = 25,570,001 bp (25.06%) number of G's = 26,720,542 bp (26.18%) number of N's = 732 bp (0%) GC percentage = 48.43% >>>>>>> Mismatches and indels general error rate = 0.0434 number of mismatches = 4,124,622 number of insertions = 109,706 mapped reads with insertion percentage = 13% number of deletions = 352,739 mapped reads with deletion percentage = 41.28% homopolymer indels = 29.8% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 8.1453X There is a 0.07% of reference with a coverageData >= 1X There is a 0.05% 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 0.03% 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 0.01% 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 9399954 0.03771286090396541 10.313885672955163 chr2 243199373 13521151 0.05559698132938854 17.0768007273343 chr3 198022430 3521653 0.017784111628162527 2.7935932019311043 chr4 191154276 3177498 0.016622688576425043 3.565620806290207 chr5 180915260 5323484 0.029425290050159394 5.412830389444855 chr6 171115067 3134636 0.018318877787658523 3.09728015071928 chr7 159138663 3049821 0.01916455085462167 2.881706556805277 chr8 146364022 3608894 0.024656974785784446 4.680828117154051 chr9 141213431 4705629 0.03332281473990955 7.40047310651153 chr10 135534747 4843561 0.03573667348934514 5.074429174709891 chr11 135006516 5401255 0.0400073652741324 6.25169466188321 chr12 133851895 5697305 0.042564246102007 8.595613664531626 chr13 115169878 3726452 0.03235613395370619 10.570691213360243 chr14 107349540 4847317 0.045154520457190594 15.680459683636034 chr15 102531392 3229677 0.03149939678961932 5.411072436244038 chr16 90354753 2057106 0.022766992678293303 2.9972089626199936 chr17 81195210 4143856 0.051035719964268825 8.947698457636061 chr18 78077248 2382927 0.0305201202788295 4.913221794929119 chr19 59128983 3463526 0.058575774929191665 7.250734704577527 chr20 63025520 2736065 0.04341201786197083 6.152515516214819 chr21 48129895 1253124 0.026036291996897148 4.411800729540089 chr22 51304566 565018 0.01101301587854773 1.6865974722559045 chrMT 16571 117771 7.107054492788607 57.14614157830042 chrX 155270560 9511745 0.061259165935899244 7.0331459454168685 chrY 59373566 834115 0.014048591927255978 2.3951407126253685