BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714184.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 = 2,125,676 number of mapped reads = 2,013,237 (94.71%) number of supplementary alignments = 134,388 (6.32%) number of secondary alignments = 0 number of mapped bases = 255,120,543 bp number of sequenced bases = 251,761,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,071,264 duplication rate = 32.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 24.8897 >>>>>>> ACTG content number of A's = 73,367,941 bp (29.14%) number of C's = 51,279,182 bp (20.37%) number of T's = 72,658,733 bp (28.86%) number of G's = 54,454,127 bp (21.63%) number of N's = 1,755 bp (0%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0395 number of mismatches = 8,054,371 number of insertions = 366,235 mapped reads with insertion percentage = 17.6% number of deletions = 547,419 mapped reads with deletion percentage = 25.61% homopolymer indels = 23.77% >>>>>>> Coverage mean coverageData = 0.0824X std coverageData = 85.3181X There is a 0.06% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 11956148 0.04796837798049057 26.399905394839212 chr2 243199373 9896952 0.04069480886367252 25.795128557709894 chr3 198022430 4776914 0.024123095550337405 13.06746210496949 chr4 191154276 6274561 0.03282459137874583 15.127374827813876 chr5 180915260 25362552 0.14019023049796905 99.81591977717036 chr6 171115067 4958775 0.02897918393124318 15.383020320912056 chr7 159138663 7986136 0.05018350568899778 26.76464477891782 chr8 146364022 1805378 0.012334848245697977 6.420158053142627 chr9 141213431 35834148 0.25375878021121095 158.53150056430917 chr10 135534747 10345641 0.07633201986203582 65.06198173684496 chr11 135006516 2893375 0.02143137298647126 11.059004539065183 chr12 133851895 1642242 0.012269097871195622 4.47060855080638 chr13 115169878 53315260 0.46292712057921953 330.6530512756614 chr14 107349540 34491291 0.3212989175361161 137.43164855832296 chr15 102531392 1889849 0.018431906200980865 9.67547892897217 chr16 90354753 983121 0.01088067829702329 5.4556067228312015 chr17 81195210 15702301 0.19338949920814294 115.27926174697068 chr18 78077248 1641848 0.021028507562151782 9.282130611051873 chr19 59128983 1846565 0.031229439545746966 16.972767153647887 chr20 63025520 4713657 0.07478965663432845 42.617656022968404 chr21 48129895 2625149 0.05454300284677538 23.76525934864773 chr22 51304566 3036064 0.05917726699023241 24.615730423592762 chrMT 16571 698 0.04212177901152616 0.34363330808201686 chrX 155270560 11049234 0.07116116538769487 26.489008421706316 chrY 59373566 92684 0.0015610313855832746 0.5199730127442901