BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714177.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 = 1,627,748 number of mapped reads = 1,562,181 (95.97%) number of supplementary alignments = 64,516 (3.96%) number of secondary alignments = 0 number of mapped bases = 203,885,198 bp number of sequenced bases = 200,133,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,454,706 duplication rate = 44.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2807 >>>>>>> ACTG content number of A's = 59,376,823 bp (29.67%) number of C's = 40,602,336 bp (20.29%) number of T's = 56,200,179 bp (28.08%) number of G's = 43,952,247 bp (21.96%) number of N's = 1,523 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0385 number of mismatches = 7,158,350 number of insertions = 202,872 mapped reads with insertion percentage = 12.63% number of deletions = 638,251 mapped reads with deletion percentage = 39.03% homopolymer indels = 26.38% >>>>>>> Coverage mean coverageData = 0.0659X std coverageData = 10.3744X There is a 0.09% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11307948 0.04536778265439106 7.237390526980022 chr2 243199373 17029159 0.07002139351732621 11.041531987071362 chr3 198022430 12698041 0.06412425602493617 8.354527394439158 chr4 191154276 12942849 0.0677089169587815 11.1665588566348 chr5 180915260 11273796 0.062315340342213255 7.8050486061688975 chr6 171115067 11717832 0.06847925320334299 11.094406008736613 chr7 159138663 10475351 0.06582530481608985 10.598243305519112 chr8 146364022 10375469 0.0708881107407666 9.957961403275068 chr9 141213431 9695744 0.0686602112231095 15.168645629095359 chr10 135534747 7548195 0.05569195477230647 7.398166075434316 chr11 135006516 9045462 0.0670001883464647 11.65022496723804 chr12 133851895 7900996 0.0590278979613998 8.937329047088637 chr13 115169878 5898342 0.05121427670523364 7.046961480903505 chr14 107349540 5712677 0.053215663523104056 8.364640867486356 chr15 102531392 5039428 0.049150098342564195 6.711897256572297 chr16 90354753 3255734 0.036032791766914575 5.035000027746605 chr17 81195210 2082566 0.025648877563097625 3.3420703349680587 chr18 78077248 5592352 0.0716258851746414 9.81506787433544 chr19 59128983 1255724 0.021237030239468182 3.2176852542697585 chr20 63025520 2389187 0.03790824732584515 4.339453669843669 chr21 48129895 2326142 0.04833050227930063 9.85502345592557 chr22 51304566 877765 0.01710890605721136 2.2925039736319306 chrMT 16571 14096 0.8506426890350612 5.8830206587758855 chrX 155270560 36405308 0.23446368712781096 23.205792753057978 chrY 59373566 1025035 0.017264164325248715 2.8806710629878