BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716201.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,231,791 number of mapped reads = 1,927,688 (86.37%) number of supplementary alignments = 52,703 (2.36%) number of secondary alignments = 0 number of mapped bases = 144,337,374 bp number of sequenced bases = 144,284,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,472 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5525 >>>>>>> ACTG content number of A's = 37,917,611 bp (26.28%) number of C's = 29,939,856 bp (20.75%) number of T's = 41,741,381 bp (28.93%) number of G's = 34,668,354 bp (24.03%) number of N's = 17,331 bp (0.01%) GC percentage = 44.78% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,101,533 number of insertions = 13,787 mapped reads with insertion percentage = 0.71% number of deletions = 30,067 mapped reads with deletion percentage = 1.54% homopolymer indels = 40.33% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.3662X There is a 4% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% of reference with a coverageData >= 7X There is a 0% 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 11943738 0.04791858873643488 0.4366690278366778 chr2 243199373 12575786 0.051709779695854725 0.5293180760202408 chr3 198022430 9565955 0.04830743163792102 0.24770820969422683 chr4 191154276 9417337 0.049265636098038426 0.2941162124534484 chr5 180915260 8926344 0.04933991748401987 0.25359802242292856 chr6 171115067 8498618 0.04966609982977127 0.2877667378069403 chr7 159138663 8012656 0.05035015280981719 0.44600620073230257 chr8 146364022 7248714 0.049525244667026166 0.45680655442779966 chr9 141213431 6291569 0.04455361615001055 0.3770790427462358 chr10 135534747 7129410 0.052602082918264494 0.4115981903684617 chr11 135006516 6656348 0.04930390174649052 0.40830103069649554 chr12 133851895 6673875 0.04986014579771172 0.25616437488698346 chr13 115169878 4604661 0.039981469807582846 0.22489510007022548 chr14 107349540 4440201 0.041362086879925146 0.28812789521634136 chr15 102531392 4277216 0.041716160451620514 0.23205594864465076 chr16 90354753 4626177 0.05120015103134641 0.2930113051987611 chr17 81195210 4347161 0.05353962382756323 0.28774768186721267 chr18 78077248 3966787 0.050805927483509664 0.7294237997975376 chr19 59128983 3243994 0.054863010243216936 0.3859899149650429 chr20 63025520 3280182 0.05204529847591896 0.27242199981122406 chr21 48129895 1907672 0.039635906124457575 0.24880653566966154 chr22 51304566 1845671 0.03597479023601915 0.21567341721003502 chrMT 16571 18695 1.1281757286826384 1.4226658973728568 chrX 155270560 4477983 0.028839871512023916 0.25593506351283096 chrY 59373566 360624 0.00607381406062085 0.2180625054708234